Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xan Working: n-5-32.cluster.ucsf.bkslab.org:/scratch/xiaobo/74215/xan-8058115.14 Result: /scratch/xiaobo/74215/xan-8058115.14 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xan Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xan mkdir: created directory `/scratch/xiaobo/74215' mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14' /scratch/xiaobo/74215/xan-8058115.14 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working' mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/protonate' Storing results in /scratch/xiaobo/74215/xan-8058115.14/finished Working in /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 /scratch/xiaobo/74215/xan-8058115.14/working/protonate /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Using inputs as protomers/tautomers. No processing done 482 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/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Bulk generating 3D conformations all protomers in /scratch/xiaobo/74215/xan-8058115.14/working/3D mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/74215/xan-8058115.14/working/protonate/xan-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 ZINC000487753128 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building' mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487753128 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/1 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1) `ZINC000487753128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487753128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000487753128 none Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 12, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 6, 5, 5, 5, 5, 49] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/2 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1) `ZINC000487753128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487753128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000487753128 none Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 12, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 6, 5, 5, 5, 5, 49] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000487753128 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/finished' Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 Building ZINC000487753128 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487753128 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 1) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1) `ZINC000487753128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487753128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000487753128 none Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 12, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 6, 5, 5, 5, 5, 49] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 2) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1) `ZINC000487753128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487753128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000487753128 none Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 12, 6, 12, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 6, 5, 5, 5, 5, 49] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000487753128 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000487753128 Building ZINC000412906357 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412906357 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/3 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1) `ZINC000412906357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412906357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000412906357 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 3, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 5, 5, 5, 23, 23, 23, 23, 23, 5, 5, 3, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 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, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/4 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1) `ZINC000412906357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412906357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000412906357 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 23, 23, 23, 23, 23, 6, 6, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 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, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412906357 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 Building ZINC000412906357 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000412906357 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 3) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1) `ZINC000412906357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412906357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000412906357 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 3, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 5, 5, 5, 23, 23, 23, 23, 23, 5, 5, 3, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 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, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 4) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1) `ZINC000412906357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412906357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000412906357 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 23, 23, 23, 23, 23, 6, 6, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 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, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412906357 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412906357 Building ZINC000801532822 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000801532822 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/5 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000801532822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532822 none Cc1cc(C)cc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 26, 13, 26, 26, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 78, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/6 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000801532822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532822 none Cc1cc(C)cc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 25, 33, 33, 33, 25, 11, 25, 25, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 25, 33, 33, 33, 33, 75, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000801532822 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 Building ZINC000801532822 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000801532822 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 5) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000801532822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532822 none Cc1cc(C)cc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 26, 13, 26, 26, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 78, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 6) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000801532822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532822 none Cc1cc(C)cc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 25, 33, 33, 33, 25, 11, 25, 25, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 25, 33, 33, 33, 33, 75, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000801532822 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532822 Building ZINC000801532823 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000801532823 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/7 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000801532823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532823 none Cc1cc(C)cc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 25, 33, 33, 33, 25, 11, 25, 25, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 25, 33, 33, 33, 33, 75, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/8 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000801532823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532823 none Cc1cc(C)cc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 26, 30, 30, 30, 26, 13, 26, 26, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 26, 30, 30, 30, 30, 78, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000801532823 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 Building ZINC000801532823 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000801532823 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 7) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000801532823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532823 none Cc1cc(C)cc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 25, 33, 33, 33, 25, 11, 25, 25, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 25, 33, 33, 33, 33, 75, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 8) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000801532823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000801532823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000801532823 none Cc1cc(C)cc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 26, 30, 30, 30, 26, 13, 26, 26, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 26, 30, 30, 30, 30, 78, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000801532823 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000801532823 Building ZINC000135692960 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000135692960 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/9 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1) `ZINC000135692960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000135692960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000135692960 none CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 19, 42, 10, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 8, 5, 5, 19, 19, 19, 42, 42, 42, 42, 19, 19, 6, 5, 5, 8, 8, 8, 5, 5, 19] 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/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/10 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1) `ZINC000135692960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000135692960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000135692960 none CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 10, 42, 6, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 8, 5, 5, 19, 19, 19, 42, 42, 42, 42, 19, 19, 6, 5, 5, 8, 8, 8, 5, 5, 19] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000135692960 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 Building ZINC000135692960 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000135692960 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 9) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1) `ZINC000135692960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000135692960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000135692960 none CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 19, 42, 10, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 8, 5, 5, 19, 19, 19, 42, 42, 42, 42, 19, 19, 6, 5, 5, 8, 8, 8, 5, 5, 19] 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/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 10) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1) `ZINC000135692960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000135692960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000135692960 none CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 10, 42, 6, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 8, 5, 5, 19, 19, 19, 42, 42, 42, 42, 19, 19, 6, 5, 5, 8, 8, 8, 5, 5, 19] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000135692960 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135692960 Building ZINC000412954733 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954733 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/11 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/12 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/13 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/13' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/14 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/14' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954733 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 Building ZINC000412954733 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954733 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 11) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 12) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 13) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 14) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954733 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 Building ZINC000412954733 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954733 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 11) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 12) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 13) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 14) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954733 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 Building ZINC000412954733 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954733 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 11) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 12) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 13) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 14) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954733 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 33, 33, 33, 33, 33, 50, 50, 33, 34, 50, 50, 33, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954733 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954733 Building ZINC000412954734 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954734 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/15 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/16 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/17 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/17' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/18 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/18' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954734 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 Building ZINC000412954734 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954734 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 15) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 16) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 17) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 18) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954734 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 Building ZINC000412954734 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954734 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 15) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 16) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 17) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 18) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954734 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 Building ZINC000412954734 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412954734 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 15) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 16) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 17) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 9, 31, 31, 31, 31, 31, 50, 50, 31, 32, 50, 50, 31, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 18) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1) `ZINC000412954734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412954734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000412954734 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(F)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 9, 28, 28, 28, 28, 28, 50, 50, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412954734 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412954734 Building ZINC000412955573 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955573 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/19 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/20 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/21 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/21' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/22 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/22' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955573 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 Building ZINC000412955573 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955573 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 19) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 20) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 21) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 22) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955573 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 Building ZINC000412955573 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955573 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 19) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 20) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 21) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 22) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955573 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 Building ZINC000412955573 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955573 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 19) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 20) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 21) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 49, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 22) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 35, 35, 35, 35, 35, 50, 50, 35, 39, 50, 50, 35, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955573 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955573 Building ZINC000412955574 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955574 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/23 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/24 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/25 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/25' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/26 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/26' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955574 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 Building ZINC000412955574 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955574 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 23) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 24) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 25) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 26) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955574 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 Building ZINC000412955574 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955574 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 23) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 24) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 25) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 26) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955574 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 Building ZINC000412955574 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000412955574 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 23) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 24) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 25) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 36, 36, 36, 36, 36, 50, 50, 36, 49, 50, 50, 36, 2, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 26) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1) `ZINC000412955574.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000412955574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000412955574 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 34, 34, 34, 34, 34, 50, 50, 34, 46, 50, 50, 34, 2, 2, 2, 2, 2, 2, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000412955574 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000412955574 Building ZINC000607864860 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607864860 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/27 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/27' -> `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[C@@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607864860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864860 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(C[C@@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 15, 21, 21, 21, 21, 21, 5, 8, 8, 8, 8, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 9, 9, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/28 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/28' -> `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[C@@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607864860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864860 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(C[C@@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 21, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 7, 7, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000607864860 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 Building ZINC000607864860 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607864860 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 27) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(C[C@@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607864860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864860 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(C[C@@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 15, 21, 21, 21, 21, 21, 5, 8, 8, 8, 8, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 9, 9, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 28) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(C[C@@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607864860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864860 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(C[C@@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 21, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 7, 7, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000607864860 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864860 Building ZINC000607864861 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607864861 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/29 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/29' -> `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[C@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607864861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864861 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(C[C@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 6, 15, 22, 22, 22, 22, 22, 6, 10, 10, 10, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 10, 10, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/30 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/30' -> `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[C@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607864861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864861 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(C[C@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 6, 19, 24, 24, 24, 24, 24, 6, 12, 12, 12, 12, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 12, 12, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000607864861 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 Building ZINC000607864861 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000607864861 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 29) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(C[C@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000607864861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864861 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(C[C@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 6, 15, 22, 22, 22, 22, 22, 6, 10, 10, 10, 10, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 10, 10, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 30) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(C[C@H]2CCCO2)C2CCCC2)cn1) `ZINC000607864861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000607864861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000607864861 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(C[C@H]2CCCO2)C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 6, 19, 24, 24, 24, 24, 24, 6, 12, 12, 12, 12, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 12, 12, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000607864861 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000607864861 Building ZINC000913661858 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913661858 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/31 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2) `ZINC000913661858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913661858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913661858 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 6, 11, 20, 20, 20, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 20, 20, 20, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/32 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2) `ZINC000913661858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913661858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913661858 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 6, 11, 20, 20, 20, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 20, 20, 20, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000913661858 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 Building ZINC000913661858 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913661858 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 31) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2) `ZINC000913661858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913661858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913661858 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 6, 11, 20, 20, 20, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 20, 20, 20, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 32) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2) `ZINC000913661858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913661858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913661858 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1C(=O)OC)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 6, 11, 20, 20, 20, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 20, 20, 20, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000913661858 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913661858 Building ZINC000194762390 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194762390 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/33 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194762390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762390 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 23, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/34 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194762390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762390 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 29, 27, 8, 27, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 16, 16, 8, 8, 16, 16, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194762390 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 Building ZINC000194762390 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194762390 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 33) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194762390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762390 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 23, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 34) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194762390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762390 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 29, 27, 8, 27, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 16, 16, 8, 8, 16, 16, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194762390 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762390 Building ZINC000194762400 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194762400 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/35 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194762400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762400 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 29, 27, 8, 27, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 16, 16, 8, 8, 16, 16, 44, 44, 44, 44, 44, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 200 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/36 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194762400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762400 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 8, 25, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 16, 16, 8, 16, 16, 16, 43, 43, 43, 43, 43, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194762400 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 Building ZINC000194762400 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194762400 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 35) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194762400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762400 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 29, 27, 8, 27, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 16, 16, 8, 8, 16, 16, 44, 44, 44, 44, 44, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 200 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 36) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1) `ZINC000194762400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194762400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194762400 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 8, 25, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 16, 16, 8, 16, 16, 16, 43, 43, 43, 43, 43, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194762400 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194762400 Building ZINC000784224316 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784224316 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/37 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784224316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224316 none CO[C@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 17, 17, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 9, 17, 17, 29, 29, 29, 17, 17, 17, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/38 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784224316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224316 none CO[C@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 8, 16, 16, 31, 31, 31, 16, 16, 16, 13, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 16, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000784224316 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 Building ZINC000784224316 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784224316 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 37) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784224316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224316 none CO[C@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 17, 17, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 9, 17, 17, 29, 29, 29, 17, 17, 17, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 38) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784224316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224316 none CO[C@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 8, 16, 16, 31, 31, 31, 16, 16, 16, 13, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 16, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000784224316 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224316 Building ZINC000784224317 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784224317 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/39 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784224317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224317 none CO[C@@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 17, 17, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 17, 17, 29, 29, 29, 17, 17, 17, 17, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/40 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784224317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224317 none CO[C@@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 17, 17, 30, 30, 30, 17, 17, 17, 17, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000784224317 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 Building ZINC000784224317 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784224317 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 39) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784224317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224317 none CO[C@@H]1Cc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 17, 17, 17, 17, 17, 17, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 17, 17, 29, 29, 29, 17, 17, 17, 17, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 40) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1) `ZINC000784224317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784224317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000784224317 none CO[C@@H]1Cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 17, 17, 30, 30, 30, 17, 17, 17, 17, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000784224317 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000784224317 Building ZINC000488020810 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020810 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/41 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020810 none CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/42 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020810 none CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 28, 28, 28, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 28, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020810 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 Building ZINC000488020810 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020810 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 41) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020810 none CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 42) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020810 none CC(C)[C@@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 28, 28, 28, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 28, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020810 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020810 Building ZINC000488020814 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020814 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/43 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020814 none CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 30, 28, 28, 28, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 28, 28, 28, 28, 28, 28, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/44 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020814 none CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 30, 29, 29, 29, 29, 29, 29, 13, 29, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 29, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020814 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 Building ZINC000488020814 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020814 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 43) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020814 none CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 30, 28, 28, 28, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 28, 28, 28, 28, 28, 28, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 44) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020814 none CC(C)[C@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 30, 29, 29, 29, 29, 29, 29, 13, 29, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 29, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020814 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020814 Building ZINC000488020815 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020815 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/45 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020815 none CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 29, 26, 26, 26, 26, 26, 26, 16, 26, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 16, 16, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/46 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020815 none CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 28, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020815 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 Building ZINC000488020815 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020815 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 45) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020815 none CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 29, 26, 26, 26, 26, 26, 26, 16, 26, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 16, 16, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 46) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020815 none CC(C)[C@@H]1OCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 28, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020815 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020815 Building ZINC000488020820 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020820 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/47 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020820 none CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 27, 26, 26, 26, 26, 26, 26, 17, 26, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 26, 26, 26, 26, 26, 26, 17, 17, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/48 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020820 none CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 29, 26, 26, 26, 26, 26, 26, 16, 26, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 16, 16, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020820 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 Building ZINC000488020820 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488020820 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 47) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488020820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020820 none CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 27, 26, 26, 26, 26, 26, 26, 17, 26, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 26, 26, 26, 26, 26, 26, 17, 17, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 48) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488020820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488020820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000488020820 none CC(C)[C@H]1OCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 26, 29, 26, 26, 26, 26, 26, 26, 16, 26, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 26, 16, 16, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488020820 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488020820 Building ZINC000608214989 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608214989 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/49 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)c2)cn1) `ZINC000608214989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608214989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214989 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 9, 9, 9, 9, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/50 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)c2)cn1) `ZINC000608214989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608214989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214989 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608214989 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 Building ZINC000608214989 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608214989 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 49) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)c2)cn1) `ZINC000608214989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608214989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214989 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 9, 9, 9, 9, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 50) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)c2)cn1) `ZINC000608214989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608214989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214989 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608214989 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214989 Building ZINC000608214990 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608214990 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/51 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)c2)cn1) `ZINC000608214990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608214990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214990 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 30, 30, 30, 30, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/52 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)c2)cn1) `ZINC000608214990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608214990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214990 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 10, 10, 10, 10, 33, 33, 33, 33, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608214990 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 Building ZINC000608214990 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608214990 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 51) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)c2)cn1) `ZINC000608214990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608214990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214990 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 30, 30, 30, 30, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 52) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)c2)cn1) `ZINC000608214990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608214990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000608214990 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]2c2cccc(F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 10, 10, 10, 10, 33, 33, 33, 33, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608214990 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608214990 Building ZINC000152168816 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152168816 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/53 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152168816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168816 none Cc1noc(C)c1[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 17, 12, 17, 17, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 17, 17, 17, 12, 12, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/54 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152168816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168816 none Cc1noc(C)c1[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 19, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 19, 19, 19, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152168816 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 Building ZINC000152168816 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152168816 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 53) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152168816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168816 none Cc1noc(C)c1[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 17, 12, 17, 17, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 17, 17, 17, 12, 12, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 54) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152168816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168816 none Cc1noc(C)c1[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 19, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 19, 19, 19, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152168816 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168816 Building ZINC000488174902 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174902 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/55 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174902 none CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 9, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 15, 15, 3, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/56 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174902 none CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 6, 16, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 8, 16, 16, 17, 16, 17, 21, 21, 21, 21, 21, 16, 16, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174902 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 Building ZINC000488174902 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174902 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 55) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174902 none CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 9, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 15, 15, 3, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 56) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174902 none CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 6, 16, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 8, 16, 16, 17, 16, 17, 21, 21, 21, 21, 21, 16, 16, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174902 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174902 Building ZINC000488174903 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174903 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/57 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174903 none CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 18, 18, 18, 18, 5, 18, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 18, 18, 20, 18, 20, 22, 22, 22, 22, 22, 18, 18, 3, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/58 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174903 none CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 19, 19, 22, 19, 22, 24, 24, 24, 24, 24, 19, 19, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174903 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 Building ZINC000488174903 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174903 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 57) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174903 none CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 18, 18, 18, 18, 5, 18, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 18, 18, 20, 18, 20, 22, 22, 22, 22, 22, 18, 18, 3, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 58) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174903 none CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 19, 19, 22, 19, 22, 24, 24, 24, 24, 24, 19, 19, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174903 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174903 Building ZINC000488174904 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174904 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/59 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174904 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 19, 19, 22, 19, 22, 24, 24, 24, 24, 24, 19, 19, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/60 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174904 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 17, 17, 20, 17, 20, 21, 21, 21, 21, 21, 17, 17, 2, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174904 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 Building ZINC000488174904 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174904 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 59) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174904 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 6, 19, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 19, 19, 22, 19, 22, 24, 24, 24, 24, 24, 19, 19, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 60) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174904 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 17, 17, 20, 17, 20, 21, 21, 21, 21, 21, 17, 17, 2, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174904 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174904 Building ZINC000488174905 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174905 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/61 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174905 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 15, 15, 16, 15, 16, 23, 23, 23, 23, 23, 15, 15, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 16, 16, 16, 16, 16, 16, 16, 16, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/62 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174905 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 17, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 9, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 17, 17, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 99 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174905 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 Building ZINC000488174905 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488174905 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 61) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488174905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174905 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 15, 15, 16, 15, 16, 23, 23, 23, 23, 23, 15, 15, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 16, 16, 16, 16, 16, 16, 16, 16, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 62) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC) `ZINC000488174905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488174905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000488174905 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 17, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 9, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 17, 17, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 99 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488174905 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488174905 Building ZINC000608248279 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608248279 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/63 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C) `ZINC000608248279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608248279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000608248279 none Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/64 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C) `ZINC000608248279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608248279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000608248279 none Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608248279 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 Building ZINC000608248279 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608248279 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 63) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C) `ZINC000608248279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608248279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000608248279 none Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 64) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C) `ZINC000608248279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608248279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000608248279 none Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608248279 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608248279 Building ZINC000413932024 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932024 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/65 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932024 none O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 17, 23, 23, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 51, 17, 17, 23, 23, 17, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/66 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932024 none O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 15, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 22, 22, 15, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932024 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 Building ZINC000413932024 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932024 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 65) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932024 none O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 17, 23, 23, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 51, 17, 17, 23, 23, 17, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 66) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932024 none O=C(N1C[C@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 15, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 22, 22, 15, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932024 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932024 Building ZINC000413932026 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932026 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/67 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932026 none O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 24, 24, 19, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 57, 19, 19, 24, 24, 19, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 127 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/68 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932026 none O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932026 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 Building ZINC000413932026 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932026 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 67) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932026 none O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 24, 24, 19, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 57, 19, 19, 24, 24, 19, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 127 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 68) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932026 none O=C(N1C[C@@H](O)C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932026 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932026 Building ZINC000413932028 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932028 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/69 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932028 none O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 15, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 22, 22, 15, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/70 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932028 none O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 25, 25, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 11, 20, 20, 60, 20, 20, 25, 25, 20, 25, 25, 7, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932028 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 Building ZINC000413932028 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932028 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 69) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932028 none O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 22, 22, 15, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 22, 22, 15, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 70) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932028 none O=C(N1C[C@@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 25, 25, 1, 1, 1, 7, 7, 11, 11, 7, 11, 11, 11, 20, 20, 60, 20, 20, 25, 25, 20, 25, 25, 7, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932028 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932028 Building ZINC000413932030 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932030 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/71 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932030 none O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 15, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 21, 21, 15, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/72 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932030 none O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 12, 21, 21, 21, 21, 21, 21, 21, 21, 27, 27, 22, 27, 27, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 21, 21, 63, 21, 21, 27, 27, 22, 27, 27, 6, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932030 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 Building ZINC000413932030 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413932030 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 71) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413932030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932030 none O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 15, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 45, 15, 15, 21, 21, 15, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 72) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000413932030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413932030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000413932030 none O=C(N1C[C@H](O)C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 12, 21, 21, 21, 21, 21, 21, 21, 21, 27, 27, 22, 27, 27, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 21, 21, 63, 21, 21, 27, 27, 22, 27, 27, 6, 10, 10, 10, 10, 10, 10, 10, 10] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413932030 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413932030 Building ZINC000413951182 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413951182 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/73 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3) `ZINC000413951182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413951182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000413951182 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 12, 12, 23, 26, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 12, 26, 26, 78, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 114 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/74 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3) `ZINC000413951182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413951182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000413951182 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 12, 12, 23, 26, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 12, 26, 26, 78, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 114 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413951182 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 Building ZINC000413951182 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000413951182 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 73) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3) `ZINC000413951182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000413951182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000413951182 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 12, 12, 23, 26, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 12, 26, 26, 78, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 114 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 74) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3) `ZINC000413951182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000413951182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000413951182 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(CO)C2CC3CC(C2)CC1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 12, 12, 23, 26, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 12, 26, 26, 78, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 114 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000413951182 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000413951182 Building ZINC000135875696 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000135875696 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/75 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1) `ZINC000135875696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000135875696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000135875696 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 6, 13, 20, 20, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 2, 6, 6, 2, 6, 6, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/76 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1) `ZINC000135875696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000135875696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000135875696 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 6, 14, 23, 23, 6, 6, 6, 6, 14, 14, 14, 14, 14, 6, 2, 6, 6, 4, 6, 6, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000135875696 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 Building ZINC000135875696 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000135875696 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 75) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1) `ZINC000135875696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000135875696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000135875696 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 6, 13, 20, 20, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 2, 6, 6, 2, 6, 6, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 76) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1) `ZINC000135875696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000135875696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000135875696 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(COC(C)C)c2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 6, 14, 23, 23, 6, 6, 6, 6, 14, 14, 14, 14, 14, 6, 2, 6, 6, 4, 6, 6, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000135875696 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000135875696 Building ZINC001118988317 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988317 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/77 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1) `ZINC001118988317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988317 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 33, 33, 33, 40, 40, 37, 40, 40, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 99, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/78 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1) `ZINC001118988317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988317 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 30, 30, 30, 41, 41, 33, 41, 41, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 90, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988317 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 Building ZINC001118988317 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988317 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 77) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1) `ZINC001118988317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988317 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 33, 33, 33, 40, 40, 37, 40, 40, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 99, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 78) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1) `ZINC001118988317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988317 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 30, 30, 30, 41, 41, 33, 41, 41, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 90, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988317 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988317 Building ZINC000414001555 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000414001555 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/79 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000414001555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000414001555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000414001555 none CC(C)OCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 27, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 46, 46, 46, 46, 46, 46, 46, 27, 27, 10, 10, 10, 10, 10, 10, 4, 3, 3, 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, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/80 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000414001555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000414001555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000414001555 none CC(C)OCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 27, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 27, 27, 10, 10, 10, 10, 10, 10, 4, 3, 3, 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, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000414001555 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 Building ZINC000414001555 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000414001555 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 79) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000414001555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000414001555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000414001555 none CC(C)OCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 27, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 46, 46, 46, 46, 46, 46, 46, 27, 27, 10, 10, 10, 10, 10, 10, 4, 3, 3, 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, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 80) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000414001555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000414001555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000414001555 none CC(C)OCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 27, 10, 4, 10, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 27, 27, 10, 10, 10, 10, 10, 10, 4, 3, 3, 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, 35, 36, 37, 38, 39]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000414001555 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000414001555 Building ZINC001118988318 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988318 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/81 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1) `ZINC001118988318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988318 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 32, 32, 32, 40, 40, 32, 40, 40, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 96, 40, 40, 32, 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, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/82 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1) `ZINC001118988318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988318 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 32, 32, 32, 39, 39, 32, 39, 39, 8, 8, 8, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 96, 39, 39, 32, 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, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988318 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 Building ZINC001118988318 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988318 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 81) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1) `ZINC001118988318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988318 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 32, 32, 32, 40, 40, 32, 40, 40, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 96, 40, 40, 32, 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, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 82) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1) `ZINC001118988318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988318 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 32, 32, 32, 39, 39, 32, 39, 39, 8, 8, 8, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 96, 39, 39, 32, 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, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988318 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988318 Building ZINC001118988319 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988319 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/83 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1) `ZINC001118988319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988319 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 35, 35, 35, 42, 42, 35, 42, 42, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 105, 42, 42, 35, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/84 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1) `ZINC001118988319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988319 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 35, 35, 35, 38, 38, 35, 38, 38, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 105, 38, 38, 35, 38, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 255 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988319 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 Building ZINC001118988319 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988319 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 83) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1) `ZINC001118988319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988319 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 35, 35, 35, 42, 42, 35, 42, 42, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 105, 42, 42, 35, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 84) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1) `ZINC001118988319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988319 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 35, 35, 35, 38, 38, 35, 38, 38, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 105, 38, 38, 35, 38, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 255 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988319 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988319 Building ZINC001118988320 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988320 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/85 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1) `ZINC001118988320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988320 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 34, 34, 34, 41, 41, 34, 41, 41, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 102, 41, 41, 34, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/86 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1) `ZINC001118988320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988320 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 40, 40, 40, 43, 43, 40, 43, 43, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 120, 43, 43, 41, 43, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988320 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 Building ZINC001118988320 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118988320 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 85) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1) `ZINC001118988320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118988320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988320 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 34, 34, 34, 41, 41, 34, 41, 41, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 102, 41, 41, 34, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 272 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 86) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1) `ZINC001118988320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118988320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001118988320 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 40, 40, 40, 43, 43, 40, 43, 43, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 120, 43, 43, 41, 43, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001118988320 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001118988320 Building ZINC000152518488 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152518488 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/87 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152518488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518488 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 49, 49, 49, 50, 50, 49, 50, 50, 49, 49, 4, 4, 4, 4, 4, 4, 4, 5, 12, 12, 12, 49, 50, 50, 49, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/88 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152518488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518488 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 48, 48, 48, 50, 50, 48, 50, 50, 48, 48, 3, 3, 3, 3, 3, 3, 3, 5, 12, 12, 12, 48, 50, 50, 48, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152518488 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 Building ZINC000152518488 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152518488 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 87) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152518488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518488 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 49, 49, 49, 50, 50, 49, 50, 50, 49, 49, 4, 4, 4, 4, 4, 4, 4, 5, 12, 12, 12, 49, 50, 50, 49, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 88) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152518488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518488 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 48, 48, 48, 50, 50, 48, 50, 50, 48, 48, 3, 3, 3, 3, 3, 3, 3, 5, 12, 12, 12, 48, 50, 50, 48, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152518488 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518488 Building ZINC000152518581 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152518581 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/89 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152518581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518581 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 47, 47, 47, 50, 50, 47, 50, 50, 47, 47, 3, 3, 3, 3, 3, 3, 3, 5, 12, 12, 12, 47, 50, 50, 47, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/90 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152518581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518581 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 49, 49, 49, 50, 50, 49, 50, 50, 49, 49, 4, 4, 4, 4, 4, 4, 4, 5, 12, 12, 12, 49, 50, 50, 49, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152518581 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 Building ZINC000152518581 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152518581 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 89) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152518581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518581 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 47, 47, 47, 50, 50, 47, 50, 50, 47, 47, 3, 3, 3, 3, 3, 3, 3, 5, 12, 12, 12, 47, 50, 50, 47, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 90) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1) `ZINC000152518581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152518581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152518581 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cn(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 49, 49, 49, 50, 50, 49, 50, 50, 49, 49, 4, 4, 4, 4, 4, 4, 4, 5, 12, 12, 12, 49, 50, 50, 49, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152518581 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152518581 Building ZINC000152549262 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549262 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/91 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/92 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/93 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/93' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/94 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/94' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549262 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 Building ZINC000152549262 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549262 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 91) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 92) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 93) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 94) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549262 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 Building ZINC000152549262 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549262 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 91) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 92) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 93) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 94) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549262 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 Building ZINC000152549262 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549262 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 91) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 92) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 93) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 94) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549262.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549262 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549262 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549262 Building ZINC000152549366 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549366 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/95 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/96 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/97 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/97' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/98 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/98' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549366 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 Building ZINC000152549366 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549366 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 95) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 96) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 97) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 98) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549366 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 Building ZINC000152549366 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549366 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 95) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 96) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 97) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 98) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549366 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 Building ZINC000152549366 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000152549366 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 95) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 96) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 97) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 50, 50, 50, 24, 24, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 98) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1) `ZINC000152549366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000152549366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152549366 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ncccc3Cl)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 16, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152549366 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152549366 Building ZINC000152593672 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152593672 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/99 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152593672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593672 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 18, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 25, 44, 44, 44, 44, 44, 18, 18, 18, 6, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44] 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]) total number of confs: 148 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/100 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152593672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593672 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 5, 1, 5, 1, 1, 1, 5, 5, 1, 3, 5, 5, 26, 44, 44, 44, 44, 44, 16, 16, 16, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44] 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]) total number of confs: 139 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152593672 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 Building ZINC000152593672 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152593672 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 99) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152593672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593672 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 18, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 25, 44, 44, 44, 44, 44, 18, 18, 18, 6, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44] 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]) total number of confs: 148 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 100) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152593672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593672 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 5, 1, 5, 1, 1, 1, 5, 5, 1, 3, 5, 5, 26, 44, 44, 44, 44, 44, 16, 16, 16, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44] 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]) total number of confs: 139 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152593672 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593672 Building ZINC000152593771 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152593771 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/101 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152593771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593771 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 18, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 43, 43, 43, 43, 43, 18, 18, 18, 5, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/102 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152593771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593771 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 20, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 28, 43, 43, 43, 43, 43, 20, 20, 20, 6, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 144 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152593771 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 Building ZINC000152593771 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152593771 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 101) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152593771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593771 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 18, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 43, 43, 43, 43, 43, 18, 18, 18, 5, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 102) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1) `ZINC000152593771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152593771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000152593771 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 20, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 28, 43, 43, 43, 43, 43, 20, 20, 20, 6, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 144 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152593771 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152593771 Building ZINC000650920163 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650920163 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/103 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650920163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920163 none O=C(N1CC[C@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 22 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/104 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650920163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920163 none O=C(N1CC[C@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 21 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650920163 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 Building ZINC000650920163 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650920163 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 103) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650920163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920163 none O=C(N1CC[C@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 22 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 104) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650920163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920163 none O=C(N1CC[C@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 21 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650920163 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920163 Building ZINC000152661194 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152661194 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/105 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1) `ZINC000152661194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152661194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152661194 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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: [11, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 6, 6, 11, 11, 11, 11, 11, 6, 2, 8, 8, 8, 16, 16, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/106 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1) `ZINC000152661194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152661194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152661194 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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: [11, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 6, 6, 11, 11, 11, 11, 11, 6, 2, 8, 8, 8, 16, 16, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152661194 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 Building ZINC000152661194 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152661194 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 105) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1) `ZINC000152661194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152661194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152661194 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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: [11, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 6, 6, 11, 11, 11, 11, 11, 6, 2, 8, 8, 8, 16, 16, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 106) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1) `ZINC000152661194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152661194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000152661194 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(OCC(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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: [11, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 6, 6, 11, 11, 11, 11, 11, 6, 2, 8, 8, 8, 16, 16, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152661194 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152661194 Building ZINC000488397053 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488397053 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/107 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1) `ZINC000488397053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488397053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000488397053 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 70 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/108 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1) `ZINC000488397053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488397053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000488397053 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488397053 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 Building ZINC000488397053 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488397053 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 107) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1) `ZINC000488397053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488397053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000488397053 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 70 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 108) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1) `ZINC000488397053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488397053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000488397053 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2ccc(=O)n(C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488397053 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488397053 Building ZINC000248028485 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028485 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/109 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/110 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/111 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/111' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/112 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/112' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028485 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 Building ZINC000248028485 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028485 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 109) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 110) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 111) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 112) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028485 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 Building ZINC000248028485 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028485 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 109) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 110) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 111) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 112) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028485 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 Building ZINC000248028485 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028485 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 109) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 110) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 21, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 111) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 112) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028485.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028485 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 21, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028485 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028485 Building ZINC000248028490 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028490 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/113 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/114 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/115 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/115' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/116 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/116' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028490 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 Building ZINC000248028490 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028490 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 113) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 114) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 115) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 116) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028490 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 Building ZINC000248028490 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028490 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 113) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 114) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 115) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 116) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028490 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 Building ZINC000248028490 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248028490 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 113) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 114) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 115) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 116) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1) `ZINC000248028490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248028490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000248028490 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 23, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248028490 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248028490 Building ZINC000194935071 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194935071 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/117 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)nc1C1CC1) `ZINC000194935071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194935071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194935071 none COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 45, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 8, 8, 19, 19, 45, 45, 45, 4, 3, 3, 1, 3, 3, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/118 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccccc2)nc1C1CC1) `ZINC000194935071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194935071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194935071 none COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccccc2)nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 8, 46, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 18, 18, 46, 46, 46, 4, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194935071 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 Building ZINC000194935071 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194935071 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 117) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)nc1C1CC1) `ZINC000194935071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194935071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194935071 none COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 45, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 8, 8, 19, 19, 45, 45, 45, 4, 3, 3, 1, 3, 3, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 118) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccccc2)nc1C1CC1) `ZINC000194935071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194935071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000194935071 none COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccccc2)nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 8, 46, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 18, 18, 46, 46, 46, 4, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194935071 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194935071 Building ZINC000488417152 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488417152 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/119 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21) `ZINC000488417152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488417152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488417152 none Cn1c(=O)ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/120 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21) `ZINC000488417152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488417152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488417152 none Cn1c(=O)ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488417152 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 Building ZINC000488417152 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488417152 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 119) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21) `ZINC000488417152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488417152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488417152 none Cn1c(=O)ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 120) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21) `ZINC000488417152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488417152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000488417152 none Cn1c(=O)ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488417152 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488417152 Building ZINC000152741590 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152741590 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/121 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152741590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741590 none COc1cccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 49, 50, 50, 50, 49, 49, 49, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 49] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/122 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152741590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741590 none COc1cccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 46, 46, 46, 46, 9, 9, 9, 9, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 46, 50, 50, 50, 46, 46, 46, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 46] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152741590 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 Building ZINC000152741590 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152741590 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 121) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152741590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741590 none COc1cccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 49, 50, 50, 50, 49, 49, 49, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 49] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 122) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152741590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741590 none COc1cccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 46, 46, 46, 46, 9, 9, 9, 9, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 46, 50, 50, 50, 46, 46, 46, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 46] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152741590 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741590 Building ZINC000152741676 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152741676 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/123 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152741676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741676 none COc1cccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 9, 9, 9, 9, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 47, 50, 50, 50, 47, 47, 47, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 47] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/124 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152741676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741676 none COc1cccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 8, 8, 8, 48, 50, 50, 50, 48, 48, 48, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 48] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152741676 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 Building ZINC000152741676 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152741676 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 123) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152741676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741676 none COc1cccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 9, 9, 9, 9, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 47, 50, 50, 50, 47, 47, 47, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 47] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 124) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1) `ZINC000152741676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152741676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152741676 none COc1cccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 8, 8, 8, 48, 50, 50, 50, 48, 48, 48, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 48] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152741676 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152741676 Building ZINC000608589551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608589551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/125 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608589551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589551 none CC(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 18, 18, 5, 12, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 25, 25, 25, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/126 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608589551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589551 none CC(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 5, 11, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 23, 23, 23, 12, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608589551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 Building ZINC000608589551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608589551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 125) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608589551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589551 none CC(C)(C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 18, 18, 5, 12, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 25, 25, 25, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 126) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608589551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589551 none CC(C)(C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 5, 11, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 23, 23, 23, 12, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608589551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589551 Building ZINC000608589552 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608589552 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/127 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608589552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589552 none CC(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 15, 4, 10, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 24, 24, 24, 12, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/128 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608589552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589552 none CC(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 4, 11, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 25, 25, 25, 12, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608589552 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 Building ZINC000608589552 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608589552 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 127) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608589552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589552 none CC(C)(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 15, 4, 10, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 24, 24, 24, 12, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 128) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F) `ZINC000608589552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608589552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000608589552 none CC(C)(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 4, 11, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 25, 25, 25, 12, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608589552 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608589552 Building ZINC000608598237 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598237 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/129 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598237 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15] 33 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: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/130 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598237 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 1, 12, 1, 1, 1, 8, 8, 14, 14, 8, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16] 41 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: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598237 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 Building ZINC000608598237 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598237 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 129) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598237 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10, 15, 15] 33 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: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 130) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598237 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 1, 12, 1, 1, 1, 8, 8, 14, 14, 8, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16] 41 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: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598237 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598237 Building ZINC000608598242 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598242 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/131 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598242 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 7, 1, 7, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 8, 8, 8, 8, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/132 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598242 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 10, 2, 12, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 8, 8, 8, 8, 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, 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/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598242 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 Building ZINC000608598242 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598242 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 131) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598242 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 7, 1, 7, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 8, 8, 8, 8, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 132) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598242 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 10, 2, 12, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 8, 8, 8, 8, 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, 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/74215/xan-8058115.14/working/building/ZINC000608598242 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598242 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598242 Building ZINC000608598246 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598246 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/133 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598246 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 1, 12, 1, 1, 1, 10, 10, 16, 16, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 42 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/134 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598246 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 26 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: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598246 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 Building ZINC000608598246 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598246 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 133) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598246 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 1, 12, 1, 1, 1, 10, 10, 16, 16, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 42 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 134) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)O1) `ZINC000608598246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598246 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 26 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: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598246 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598246 Building ZINC000608598248 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598248 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/135 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598248 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 11, 1, 11, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27] 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/136 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598248 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 7, 1, 10, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27] 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598248 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 Building ZINC000608598248 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608598248 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 135) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608598248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598248 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 11, 1, 11, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27] 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 136) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)O1) `ZINC000608598248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608598248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000608598248 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C[C@@H](C(F)(F)F)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', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 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, 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, 7, 1, 10, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27] 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000608598248 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000608598248 Building ZINC000746206796 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746206796 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/137 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1) `ZINC000746206796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746206796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000746206796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 14, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 38, 38] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/138 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1) `ZINC000746206796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746206796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000746206796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000746206796 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 Building ZINC000746206796 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746206796 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 137) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1) `ZINC000746206796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746206796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000746206796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 14, 38, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 38, 38, 38, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 38, 38] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 138) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1) `ZINC000746206796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746206796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000746206796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc(c3ccccc3)ncc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 35, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000746206796 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746206796 Building ZINC000680380111 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680380111 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/139 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000680380111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680380111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000680380111 none COCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 44, 25, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 48, 48, 25, 25, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/140 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000680380111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680380111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000680380111 none COCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 42, 24, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 47, 47, 24, 24, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680380111 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 Building ZINC000680380111 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680380111 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 139) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000680380111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680380111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000680380111 none COCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 44, 25, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 48, 48, 25, 25, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 140) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000680380111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680380111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000680380111 none COCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 42, 24, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 47, 47, 24, 24, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680380111 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680380111 Building ZINC001125803122 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001125803122 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/141 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/141' -> `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])c1cc(Cl)cc(Cl)c1)C(=O)OC) `ZINC001125803122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001125803122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001125803122 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 29, 4, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 23, 23, 23, 30, 30, 30, 30, 30, 29, 29, 29, 4, 3, 1, 3, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/142 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/142' -> `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])c1cc(Cl)cc(Cl)c1)C(=O)OC) `ZINC001125803122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001125803122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001125803122 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 11, 31, 31, 3, 11, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 24, 24, 24, 32, 32, 32, 32, 32, 31, 31, 31, 3, 3, 1, 3, 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]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001125803122 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 Building ZINC001125803122 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001125803122 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 141) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC) `ZINC001125803122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001125803122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001125803122 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 29, 4, 11, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 23, 23, 23, 30, 30, 30, 30, 30, 29, 29, 29, 4, 3, 1, 3, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 142) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC) `ZINC001125803122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001125803122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001125803122 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 11, 31, 31, 3, 11, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 24, 24, 24, 32, 32, 32, 32, 32, 31, 31, 31, 3, 3, 1, 3, 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]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001125803122 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125803122 Building ZINC000680388654 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680388654 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/143 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000680388654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680388654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680388654 none CN(C)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 23, 15, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/144 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000680388654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680388654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680388654 none CN(C)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 42, 25, 19, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 49, 49, 42, 42, 25, 25, 8, 8, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680388654 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 Building ZINC000680388654 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680388654 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 143) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000680388654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680388654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680388654 none CN(C)CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 23, 15, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 144) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000680388654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680388654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680388654 none CN(C)CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 42, 25, 19, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 49, 49, 42, 42, 25, 25, 8, 8, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680388654 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680388654 Building ZINC000746313535 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746313535 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/145 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746313535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313535 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 28, 38, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 23, 23, 21, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 21, 23, 23] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/146 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746313535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313535 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 35, 43, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 30, 30, 27, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 27, 30, 30] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000746313535 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 Building ZINC000746313535 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746313535 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 145) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746313535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313535 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 28, 38, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 23, 23, 21, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 21, 23, 23] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 146) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746313535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313535 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 35, 43, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 30, 30, 27, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 27, 30, 30] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000746313535 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313535 Building ZINC000746313538 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746313538 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/147 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746313538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313538 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 37, 45, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 29, 29, 26, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 26, 29, 29] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/148 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746313538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313538 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 30, 39, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 23, 23, 21, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 21, 23, 23] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000746313538 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 Building ZINC000746313538 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746313538 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 147) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746313538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313538 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 37, 45, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 29, 29, 26, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 26, 29, 29] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 148) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1) `ZINC000746313538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746313538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000746313538 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 30, 39, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 23, 23, 21, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 21, 23, 23] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000746313538 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000746313538 Building ZINC000488698289 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488698289 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/149 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)cn1) `ZINC000488698289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488698289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698289 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)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', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 13, 13, 33, 33, 33, 33, 33, 33, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/150 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)cn1) `ZINC000488698289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488698289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698289 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)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', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 14, 14, 36, 36, 36, 36, 36, 36, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488698289 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 Building ZINC000488698289 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488698289 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 149) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)cn1) `ZINC000488698289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488698289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698289 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)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', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 13, 13, 33, 33, 33, 33, 33, 33, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 150) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)cn1) `ZINC000488698289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488698289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698289 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2[C@@H]3Cc4ccccc4[C@H]23)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', 'H', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 14, 14, 36, 36, 36, 36, 36, 36, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488698289 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698289 Building ZINC000488698292 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488698292 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/151 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)cn1) `ZINC000488698292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698292 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)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', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 37, 37, 37, 37, 37, 37, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/152 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)cn1) `ZINC000488698292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698292 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)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', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 14, 14, 35, 35, 35, 35, 35, 35, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488698292 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 Building ZINC000488698292 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488698292 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 151) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)cn1) `ZINC000488698292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698292 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)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', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 37, 37, 37, 37, 37, 37, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 152) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)cn1) `ZINC000488698292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000488698292 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2[C@@H]3c4ccccc4C[C@H]23)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', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 14, 14, 35, 35, 35, 35, 35, 35, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000488698292 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000488698292 Building ZINC001119050014 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119050014 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/153 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1) `ZINC001119050014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119050014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001119050014 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 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, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/154 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1) `ZINC001119050014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119050014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001119050014 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 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, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001119050014 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 Building ZINC001119050014 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119050014 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 153) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1) `ZINC001119050014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119050014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001119050014 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 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, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 154) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1) `ZINC001119050014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119050014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001119050014 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 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, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001119050014 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001119050014 Building ZINC000153110857 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153110857 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/155 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1) `ZINC000153110857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153110857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153110857 none COC(=O)C1(N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 28, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 28, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/156 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1) `ZINC000153110857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153110857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153110857 none COC(=O)C1(N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 26, 26, 26, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153110857 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 Building ZINC000153110857 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153110857 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 155) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1) `ZINC000153110857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153110857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153110857 none COC(=O)C1(N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 28, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 28, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 156) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1) `ZINC000153110857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153110857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153110857 none COC(=O)C1(N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 26, 26, 26, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153110857 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153110857 Building ZINC000153188219 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153188219 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/157 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/157' -> `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(Cc1ccccc1F)C1CCC1) `ZINC000153188219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153188219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000153188219 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 21, 34, 34, 27, 34, 34, 34, 10, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/158 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/158' -> `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(Cc1ccccc1F)C1CCC1) `ZINC000153188219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153188219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000153188219 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 20, 31, 31, 24, 31, 31, 31, 10, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 31, 31, 31, 31, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153188219 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 Building ZINC000153188219 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153188219 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 157) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1F)C1CCC1) `ZINC000153188219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153188219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000153188219 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 21, 34, 34, 27, 34, 34, 34, 10, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 158) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1F)C1CCC1) `ZINC000153188219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153188219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000153188219 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 20, 31, 31, 24, 31, 31, 31, 10, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 31, 31, 31, 31, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153188219 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153188219 Building ZINC000178034806 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178034806 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/159 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178034806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000178034806 none CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 31, 31, 31, 31, 31, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/160 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178034806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000178034806 none CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 14, 27, 14, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000178034806 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 Building ZINC000178034806 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178034806 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 159) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178034806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000178034806 none CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 31, 31, 31, 31, 31, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 160) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178034806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000178034806 none CC[S@](=O)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 14, 27, 14, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000178034806 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000178034806 Building ZINC000489005372 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489005372 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/161 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489005372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005372 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 3, 22, 22, 22, 22, 22, 22, 22, 22, 9, 12, 12, 9, 12, 12, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/162 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489005372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005372 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 3, 23, 23, 23, 23, 23, 23, 23, 23, 9, 13, 13, 9, 13, 13, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489005372 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 Building ZINC000489005372 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489005372 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 161) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489005372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005372 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 3, 22, 22, 22, 22, 22, 22, 22, 22, 9, 12, 12, 9, 12, 12, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 162) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489005372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005372 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 3, 23, 23, 23, 23, 23, 23, 23, 23, 9, 13, 13, 9, 13, 13, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489005372 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005372 Building ZINC000489005374 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489005374 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/163 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489005374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005374 none O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 14, 14, 9, 14, 14, 9, 4, 22, 22, 22, 22, 22, 22, 22, 22, 9, 14, 14, 9, 14, 14, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/164 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489005374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005374 none O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 4, 22, 22, 22, 22, 22, 22, 22, 22, 10, 12, 12, 10, 12, 12, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489005374 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 Building ZINC000489005374 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489005374 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 163) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489005374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005374 none O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 14, 14, 9, 14, 14, 9, 4, 22, 22, 22, 22, 22, 22, 22, 22, 9, 14, 14, 9, 14, 14, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 164) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000489005374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489005374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489005374 none O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 4, 22, 22, 22, 22, 22, 22, 22, 22, 10, 12, 12, 10, 12, 12, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489005374 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489005374 Building ZINC000153325504 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153325504 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/165 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ncccc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000153325504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153325504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153325504 none O=C(NCCOc1ncccc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 17, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 17, 17, 31, 31, 31, 4, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/166 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ncccc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000153325504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153325504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153325504 none O=C(NCCOc1ncccc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 17, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 17, 17, 30, 30, 30, 4, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153325504 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 Building ZINC000153325504 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153325504 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 165) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ncccc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000153325504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153325504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153325504 none O=C(NCCOc1ncccc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 17, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 17, 17, 31, 31, 31, 4, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 166) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ncccc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000153325504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153325504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153325504 none O=C(NCCOc1ncccc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 17, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 17, 17, 30, 30, 30, 4, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153325504 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153325504 Building ZINC000153381340 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153381340 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/167 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nnc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000153381340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153381340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153381340 none O=C(Nc1ccc2[nH]nnc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 38, 38, 38, 6, 6, 6, 6] 43 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/168 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nnc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000153381340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153381340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153381340 none O=C(Nc1ccc2[nH]nnc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 38, 38, 38, 6, 6, 6, 6] 43 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153381340 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 Building ZINC000153381340 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153381340 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 167) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nnc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000153381340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153381340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153381340 none O=C(Nc1ccc2[nH]nnc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 38, 38, 38, 6, 6, 6, 6] 43 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 168) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nnc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000153381340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153381340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000153381340 none O=C(Nc1ccc2[nH]nnc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 38, 38, 38, 6, 6, 6, 6] 43 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153381340 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153381340 Building ZINC000153403140 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153403140 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/169 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1) `ZINC000153403140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153403140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153403140 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 9, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 9, 9, 3, 3, 12, 12, 12, 12, 12, 3, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/170 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1) `ZINC000153403140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153403140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153403140 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 9, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 9, 9, 3, 3, 12, 12, 12, 12, 12, 3, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153403140 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 Building ZINC000153403140 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153403140 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 169) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1) `ZINC000153403140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153403140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153403140 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 9, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 9, 9, 3, 3, 12, 12, 12, 12, 12, 3, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 170) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1) `ZINC000153403140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153403140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000153403140 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(C(C)(C)C)ccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 9, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 9, 9, 3, 3, 12, 12, 12, 12, 12, 3, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153403140 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153403140 Building ZINC000106494389 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494389 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/171 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106494389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106494389 none O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 161 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/172 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106494389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106494389 none O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494389 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 Building ZINC000106494389 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494389 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 171) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106494389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106494389 none O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 161 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 172) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106494389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106494389 none O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494389 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494389 Building ZINC000106500445 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106500445 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/173 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106500445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106500445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000106500445 none O=C(NCCOc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 15, 35, 50, 50, 35, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 15, 15, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/174 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106500445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106500445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000106500445 none O=C(NCCOc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 15, 34, 50, 50, 34, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 15, 15, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106500445 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 Building ZINC000106500445 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106500445 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 173) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106500445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106500445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000106500445 none O=C(NCCOc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 15, 35, 50, 50, 35, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 15, 15, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 174) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000106500445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106500445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000106500445 none O=C(NCCOc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 15, 34, 50, 50, 34, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 15, 15, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106500445 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500445 Building ZINC000489095298 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489095298 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/175 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(O)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000489095298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489095298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489095298 none CSc1cc(O)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 9, 9, 7, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 20, 20, 20, 9, 18, 9, 9, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/176 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(O)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000489095298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489095298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489095298 none CSc1cc(O)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [21, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 21, 21, 21, 9, 18, 9, 9, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489095298 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 Building ZINC000489095298 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489095298 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 175) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(O)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000489095298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489095298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489095298 none CSc1cc(O)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 9, 9, 7, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 20, 20, 20, 9, 18, 9, 9, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 176) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(O)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000489095298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489095298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000489095298 none CSc1cc(O)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 14, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [21, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 21, 21, 21, 9, 18, 9, 9, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489095298 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489095298 Building ZINC000416005058 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416005058 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/177 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)cn1) `ZINC000416005058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416005058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416005058 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)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.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 15, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 10, 10, 1, 1, 1, 2, 11, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 21, 21, 21, 21, 21, 21, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/178 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)cn1) `ZINC000416005058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416005058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416005058 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)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.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 15, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 22, 22, 12, 12, 1, 1, 1, 2, 11, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 20, 20, 20, 20, 20, 20, 12] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416005058 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 Building ZINC000416005058 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416005058 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 177) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)cn1) `ZINC000416005058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416005058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416005058 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)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.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 15, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 10, 10, 1, 1, 1, 2, 11, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 21, 21, 21, 21, 21, 21, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 178) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)cn1) `ZINC000416005058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416005058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416005058 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)c(F)ccc32)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.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 15, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 22, 22, 12, 12, 1, 1, 1, 2, 11, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 20, 20, 20, 20, 20, 20, 12] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416005058 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416005058 Building ZINC000416048117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416048117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/179 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416048117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048117 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 18, 18, 18, 18, 3, 3, 9, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 10, 10, 18, 18, 18, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/180 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416048117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048117 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 5, 5, 5, 5, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 4, 4, 12, 12, 12, 12, 12, 4, 5, 5, 5, 5, 5, 5, 9, 9, 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, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416048117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 Building ZINC000416048117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416048117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 179) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416048117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048117 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 18, 18, 18, 18, 3, 3, 9, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 10, 10, 18, 18, 18, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 180) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416048117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048117 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 5, 5, 5, 5, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 4, 4, 12, 12, 12, 12, 12, 4, 5, 5, 5, 5, 5, 5, 9, 9, 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, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416048117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048117 Building ZINC000416048121 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416048121 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/181 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416048121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048121 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 7, 7, 11, 19, 19, 19, 19, 19, 19, 19, 4, 4, 13, 13, 13, 13, 13, 4, 7, 7, 7, 7, 7, 7, 11, 11, 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, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/182 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416048121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048121 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 9, 19, 19, 19, 19, 19, 19, 19, 3, 3, 8, 8, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 9, 9, 19, 19, 19, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416048121 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 Building ZINC000416048121 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416048121 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 181) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416048121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048121 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 7, 7, 11, 19, 19, 19, 19, 19, 19, 19, 4, 4, 13, 13, 13, 13, 13, 4, 7, 7, 7, 7, 7, 7, 11, 11, 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, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 182) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1) `ZINC000416048121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416048121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000416048121 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2cc(F)ccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 9, 19, 19, 19, 19, 19, 19, 19, 3, 3, 8, 8, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 9, 9, 19, 19, 19, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416048121 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416048121 Building ZINC000416054732 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416054732 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/183 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416054732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054732 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 25, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 47, 47, 46, 46, 46, 46, 25, 25, 4, 3, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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]) total number of confs: 220 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/184 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416054732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054732 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 43, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 46, 46, 44, 44, 44, 44, 25, 25, 4, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416054732 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 Building ZINC000416054732 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416054732 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 183) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416054732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054732 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 25, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 47, 47, 46, 46, 46, 46, 25, 25, 4, 3, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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]) total number of confs: 220 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 184) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416054732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054732 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 43, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 46, 46, 44, 44, 44, 44, 25, 25, 4, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 234 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416054732 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054732 Building ZINC000416054733 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416054733 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/185 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054733 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 43, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 41, 46, 46, 44, 44, 44, 44, 25, 25, 4, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 233 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/186 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054733 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 16, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 34, 45, 46, 46, 36, 36, 36, 16, 16, 3, 3, 3, 3, 3, 45, 45, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 222 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416054733 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 Building ZINC000416054733 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416054733 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 185) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054733 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 43, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 41, 46, 46, 44, 44, 44, 44, 25, 25, 4, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 233 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 186) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C) `ZINC000416054733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000416054733 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 16, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 34, 45, 46, 46, 36, 36, 36, 16, 16, 3, 3, 3, 3, 3, 45, 45, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 222 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416054733 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416054733 Building ZINC000107159669 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107159669 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/187 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/187' -> `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)Cc1ccc(F)cc1Cl) `ZINC000107159669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107159669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107159669 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 25, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/188 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/188' -> `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)Cc1ccc(F)cc1Cl) `ZINC000107159669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107159669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107159669 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 24, 40, 40, 33, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 24, 24, 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]) total number of confs: 150 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000107159669 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 Building ZINC000107159669 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107159669 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 187) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Cl) `ZINC000107159669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107159669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107159669 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 25, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 188) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Cl) `ZINC000107159669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107159669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000107159669 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 24, 40, 40, 33, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 24, 24, 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]) total number of confs: 150 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000107159669 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107159669 Building ZINC000609299842 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000609299842 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/189 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000609299842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000609299842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000609299842 none COC(=O)c1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 30, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 30, 30, 30, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/190 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000609299842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000609299842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000609299842 none COC(=O)c1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 31, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 31, 31, 31, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000609299842 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 Building ZINC000609299842 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000609299842 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 189) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000609299842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000609299842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000609299842 none COC(=O)c1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 30, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 30, 30, 30, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 190) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000609299842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000609299842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000609299842 none COC(=O)c1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 31, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 31, 31, 31, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000609299842 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000609299842 Building ZINC000248724710 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724710 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/191 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/192 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/193 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/193' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/194 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/194' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724710 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 Building ZINC000248724710 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724710 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 191) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 192) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 193) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 194) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724710 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 Building ZINC000248724710 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724710 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 191) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 192) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 193) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 194) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724710 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 Building ZINC000248724710 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724710 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 191) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 192) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 193) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 194) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724710 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 24, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724710 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724710 Building ZINC000248724716 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724716 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/195 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/196 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/197 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/197' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/198 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/198' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724716 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 Building ZINC000248724716 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724716 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 195) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 196) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 197) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 198) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724716 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 Building ZINC000248724716 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724716 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 195) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 196) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 197) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 198) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724716 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 Building ZINC000248724716 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000248724716 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 195) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 196) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 29, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 197) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 198) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1) `ZINC000248724716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000248724716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000248724716 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000248724716 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000248724716 Building ZINC000107524947 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107524947 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/199 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107524947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524947 none O=C(N1CCCC[C@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 22, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 29, 29, 29, 29, 22, 22, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/200 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107524947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524947 none O=C(N1CCCC[C@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 22, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 29, 29, 29, 29, 22, 22, 5, 8, 8, 8, 8, 8, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000107524947 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 Building ZINC000107524947 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107524947 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 199) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107524947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524947 none O=C(N1CCCC[C@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 22, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 29, 29, 29, 29, 22, 22, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 200) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107524947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524947 none O=C(N1CCCC[C@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 22, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 29, 29, 29, 29, 29, 29, 29, 29, 22, 22, 5, 8, 8, 8, 8, 8, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000107524947 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524947 Building ZINC000107524948 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107524948 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/201 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107524948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524948 none O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 23, 23, 29, 29, 29, 29, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/202 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107524948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524948 none O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 23, 23, 23, 23, 23, 23, 31, 31, 31, 31, 23, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 4, 8, 8, 8, 8, 8, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000107524948 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 Building ZINC000107524948 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000107524948 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 201) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107524948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524948 none O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 23, 23, 29, 29, 29, 29, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 202) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000107524948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107524948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000107524948 none O=C(N1CCCC[C@@H](N2CCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 23, 23, 23, 23, 23, 23, 31, 31, 31, 31, 23, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 4, 8, 8, 8, 8, 8, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000107524948 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000107524948 Building ZINC000416108597 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416108597 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/203 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1) `ZINC000416108597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416108597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000416108597 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 18, 18, 18, 28, 28, 28, 28, 28, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 26, 26, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/204 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1) `ZINC000416108597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416108597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000416108597 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 17, 17, 17, 27, 28, 28, 28, 28, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 25, 25, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416108597 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 Building ZINC000416108597 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416108597 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 203) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1) `ZINC000416108597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416108597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000416108597 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 18, 18, 18, 28, 28, 28, 28, 28, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 26, 26, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 204) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1) `ZINC000416108597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416108597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000416108597 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 17, 17, 17, 27, 28, 28, 28, 28, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 25, 25, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416108597 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416108597 Building ZINC000416119745 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416119745 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/205 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1) `ZINC000416119745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416119745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119745 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 11, 11, 13, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/206 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1) `ZINC000416119745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416119745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119745 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 20, 9, 9, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 12, 21, 21, 21, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416119745 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 Building ZINC000416119745 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416119745 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 205) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1) `ZINC000416119745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416119745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119745 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 17, 17, 8, 8, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 11, 11, 13, 22, 22, 22, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 206) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1) `ZINC000416119745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416119745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119745 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 20, 9, 9, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 12, 21, 21, 21, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416119745 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119745 Building ZINC000416119750 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416119750 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/207 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1) `ZINC000416119750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416119750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119750 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 13, 21, 21, 21, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/208 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1) `ZINC000416119750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416119750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119750 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 7, 7, 1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 13, 14, 25, 25, 25, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416119750 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 Building ZINC000416119750 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416119750 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 207) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1) `ZINC000416119750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416119750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119750 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 13, 21, 21, 21, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 208) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1) `ZINC000416119750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416119750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000416119750 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2C2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 7, 7, 1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 13, 14, 25, 25, 25, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416119750 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416119750 Building ZINC000108202706 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108202706 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/209 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1) `ZINC000108202706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108202706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000108202706 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 41, 42, 43, 44, 45]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/210 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1) `ZINC000108202706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108202706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000108202706 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 11, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 11, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000108202706 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 Building ZINC000108202706 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108202706 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 209) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1) `ZINC000108202706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108202706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000108202706 none Cc1ccc(N(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 41, 42, 43, 44, 45]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 210) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1) `ZINC000108202706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108202706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000108202706 none Cc1ccc(N(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C2CCCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 11, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 11, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000108202706 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000108202706 Building ZINC000091835073 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000091835073 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/211 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12) `ZINC000091835073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000091835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000091835073 none Cc1n[nH]c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 4, 11, 11, 11, 11, 11, 11, 11, 17, 17] 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: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/212 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12) `ZINC000091835073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000091835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000091835073 none Cc1n[nH]c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 4, 11, 11, 11, 11, 11, 11, 11, 17, 17] 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: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000091835073 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 Building ZINC000091835073 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000091835073 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 211) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12) `ZINC000091835073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000091835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000091835073 none Cc1n[nH]c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 4, 11, 11, 11, 11, 11, 11, 11, 17, 17] 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: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 212) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12) `ZINC000091835073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000091835073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000091835073 none Cc1n[nH]c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 4, 11, 11, 11, 11, 11, 11, 11, 17, 17] 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: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000091835073 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000091835073 Building ZINC000416125018 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416125018 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/213 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000416125018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416125018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000416125018 none COCCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 15, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 27, 28, 16, 16, 11, 11, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/214 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000416125018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416125018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000416125018 none COCCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 15, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 28, 27, 16, 16, 11, 11, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416125018 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 Building ZINC000416125018 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416125018 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 213) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000416125018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416125018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000416125018 none COCCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 15, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 27, 28, 16, 16, 11, 11, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 214) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000416125018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416125018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000416125018 none COCCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 15, 11, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 28, 27, 16, 16, 11, 11, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416125018 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416125018 Building ZINC000907963447 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907963447 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/215 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C) `ZINC000907963447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907963447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907963447 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 15, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/216 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C) `ZINC000907963447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907963447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907963447 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 14, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000907963447 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 Building ZINC000907963447 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907963447 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 215) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C) `ZINC000907963447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907963447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907963447 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 15, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 216) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C) `ZINC000907963447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907963447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907963447 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(O[C@@H]2CCN(C)C2=O)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 14, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000907963447 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907963447 Building ZINC000195178446 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195178446 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/217 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/217' -> `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)c1c(Cl)ccc(F)c1Cl) `ZINC000195178446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195178446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178446 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 5, 7, 7, 7, 7, 7, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/218 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/218' -> `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)c1c(Cl)ccc(F)c1Cl) `ZINC000195178446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195178446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178446 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 5, 8, 8, 8, 8, 8, 23, 23] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195178446 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 Building ZINC000195178446 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195178446 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 217) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl) `ZINC000195178446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195178446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178446 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 5, 7, 7, 7, 7, 7, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 218) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl) `ZINC000195178446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195178446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178446 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 5, 8, 8, 8, 8, 8, 23, 23] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195178446 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178446 Building ZINC000195178456 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195178456 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/219 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/219' -> `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)c1c(Cl)ccc(F)c1Cl) `ZINC000195178456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195178456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178456 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 5, 8, 8, 8, 8, 8, 23, 23] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/220 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/220' -> `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)c1c(Cl)ccc(F)c1Cl) `ZINC000195178456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195178456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178456 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 5, 7, 7, 7, 7, 7, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195178456 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 Building ZINC000195178456 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195178456 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 219) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl) `ZINC000195178456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195178456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178456 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 5, 8, 8, 8, 8, 8, 23, 23] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 220) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl) `ZINC000195178456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195178456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000195178456 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1c(Cl)ccc(F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 16, 1, 1, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 9, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 5, 7, 7, 7, 7, 7, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195178456 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195178456 Building ZINC000489254151 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254151 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/221 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254151 none CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 16, 25, 25, 16, 16, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 26, 26, 26, 26, 26, 25, 25, 25, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/222 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254151 none CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 17, 27, 27, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 28, 28, 28, 28, 28, 27, 27, 27, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254151 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 Building ZINC000489254151 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254151 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 221) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254151 none CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 16, 25, 25, 16, 16, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 26, 26, 26, 26, 26, 25, 25, 25, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 222) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254151 none CC[C@@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 17, 27, 27, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 28, 28, 28, 28, 28, 27, 27, 27, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254151 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254151 Building ZINC000489254152 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254152 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/223 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254152 none CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 17, 28, 28, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 29, 29, 29, 29, 29, 28, 28, 28, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/224 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254152 none CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 16, 25, 25, 16, 16, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 26, 26, 26, 26, 26, 25, 25, 25, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254152 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 Building ZINC000489254152 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254152 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 223) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254152 none CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 17, 28, 28, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 29, 29, 29, 29, 29, 28, 28, 28, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 224) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254152 none CC[C@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 16, 25, 25, 16, 16, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 26, 26, 26, 26, 26, 25, 25, 25, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254152 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254152 Building ZINC000489254153 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254153 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/225 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254153 none CC[C@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 27, 27, 17, 17, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/226 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254153 none CC[C@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 17, 28, 28, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 29, 29, 29, 29, 29, 28, 28, 28, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254153 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 Building ZINC000489254153 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254153 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 225) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254153 none CC[C@H](C)c1nc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 27, 27, 17, 17, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 226) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254153 none CC[C@H](C)c1nc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 17, 28, 28, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 29, 29, 29, 29, 29, 28, 28, 28, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254153 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254153 Building ZINC000489254154 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254154 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/227 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254154 none CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/228 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254154 none CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 16, 26, 26, 16, 16, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254154 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 Building ZINC000489254154 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489254154 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 227) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489254154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254154 none CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 17, 17, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 228) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1) `ZINC000489254154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489254154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000489254154 none CC[C@@H](C)c1nc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 8, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 16, 26, 26, 16, 16, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489254154 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489254154 Building ZINC000377572233 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377572233 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/229 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)Oc1ccccc1O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000377572233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377572233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000377572233 none O=C(N1CCC2(C1)Oc1ccccc1O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5] 39 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/230 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)Oc1ccccc1O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000377572233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377572233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000377572233 none O=C(N1CCC2(C1)Oc1ccccc1O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 1, 1, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 5, 5] 40 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000377572233 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 Building ZINC000377572233 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000377572233 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 229) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)Oc1ccccc1O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000377572233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000377572233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000377572233 none O=C(N1CCC2(C1)Oc1ccccc1O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5] 39 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 230) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C1)Oc1ccccc1O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000377572233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000377572233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000377572233 none O=C(N1CCC2(C1)Oc1ccccc1O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 1, 1, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 5, 5] 40 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000377572233 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000377572233 Building ZINC000416201773 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416201773 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/231 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)c2)cn1) `ZINC000416201773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416201773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416201773 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 12, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 2, 2, 2, 11, 11, 11, 11, 26, 11, 11, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 26, 26, 78, 11, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/232 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)c2)cn1) `ZINC000416201773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416201773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416201773 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 12, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 9, 11, 23, 11, 11, 11, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 11, 11, 23, 23, 69, 11, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416201773 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 Building ZINC000416201773 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416201773 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 231) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)c2)cn1) `ZINC000416201773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416201773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416201773 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 12, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 2, 2, 2, 11, 11, 11, 11, 26, 11, 11, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 26, 26, 78, 11, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 232) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)c2)cn1) `ZINC000416201773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416201773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000416201773 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CO)c(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 12, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 9, 11, 23, 11, 11, 11, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 11, 11, 23, 23, 69, 11, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416201773 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416201773 Building ZINC000416254221 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416254221 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/233 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OC2CCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416254221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416254221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000416254221 none O=C(N1CCC(OC2CCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 16, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 6, 11, 11, 11, 11, 11, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/234 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OC2CCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416254221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416254221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000416254221 none O=C(N1CCC(OC2CCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 19, 29, 29, 29, 6, 6, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416254221 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 Building ZINC000416254221 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416254221 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 233) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OC2CCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416254221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416254221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000416254221 none O=C(N1CCC(OC2CCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 16, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 6, 11, 11, 11, 11, 11, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 234) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OC2CCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000416254221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416254221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000416254221 none O=C(N1CCC(OC2CCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 6, 6, 6, 6, 19, 29, 29, 29, 6, 6, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416254221 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416254221 Building ZINC000416259937 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416259937 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/235 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F) `ZINC000416259937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416259937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259937 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 36, 36, 36] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/236 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F) `ZINC000416259937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416259937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259937 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 26, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 26, 26, 41, 41, 41] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416259937 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 Building ZINC000416259937 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416259937 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 235) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F) `ZINC000416259937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416259937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259937 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 9, 9, 9, 9, 9, 9, 20, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 20, 20, 36, 36, 36] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 236) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F) `ZINC000416259937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416259937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259937 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 26, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 26, 26, 41, 41, 41] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416259937 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259937 Building ZINC000416259939 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416259939 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/237 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F) `ZINC000416259939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416259939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259939 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 25, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 25, 25, 43, 43, 43] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/238 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F) `ZINC000416259939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416259939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259939 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 20, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 20, 20, 35, 35, 35] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416259939 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 Building ZINC000416259939 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416259939 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 237) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F) `ZINC000416259939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416259939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259939 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 25, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 25, 25, 43, 43, 43] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 238) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F) `ZINC000416259939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416259939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000416259939 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1cc(F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 20, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 20, 20, 35, 35, 35] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416259939 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416259939 Building ZINC000416270032 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416270032 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/239 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC000416270032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416270032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000416270032 none COC1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [38, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 22, 22, 38, 38, 38, 22, 22, 22, 22, 5, 5, 5, 5, 22, 22, 22, 22] 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: 79 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/240 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC000416270032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416270032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000416270032 none COC1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [36, 22, 22, 22, 22, 22, 22, 22, 22, 7, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 22, 36, 36, 36, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22, 22, 22] 38 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: 79 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416270032 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 Building ZINC000416270032 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416270032 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 239) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC000416270032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416270032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000416270032 none COC1(C(F)(F)F)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [38, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 22, 22, 38, 38, 38, 22, 22, 22, 22, 5, 5, 5, 5, 22, 22, 22, 22] 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: 79 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 240) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC000416270032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416270032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000416270032 none COC1(C(F)(F)F)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [36, 22, 22, 22, 22, 22, 22, 22, 22, 7, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 22, 36, 36, 36, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22, 22, 22] 38 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: 79 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416270032 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416270032 Building ZINC000416356950 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416356950 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/241 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416356950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356950 none Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 15, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/242 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416356950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356950 none Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 14, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 14, 14, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416356950 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 Building ZINC000416356950 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416356950 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 241) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416356950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356950 none Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 15, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 242) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416356950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356950 none Cc1ncccc1OC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 14, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 14, 14, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416356950 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356950 Building ZINC000416356953 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416356953 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/243 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416356953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356953 none Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 13, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 13, 13, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/244 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416356953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356953 none Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 15, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416356953 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 Building ZINC000416356953 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416356953 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 243) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416356953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356953 none Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 13, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 13, 13, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 244) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000416356953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416356953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000416356953 none Cc1ncccc1OC[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 15, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416356953 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416356953 Building ZINC000416363055 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416363055 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/245 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1) `ZINC000416363055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416363055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363055 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 14, 39, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/246 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1) `ZINC000416363055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416363055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363055 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 14, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 14, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416363055 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 Building ZINC000416363055 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416363055 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 245) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1) `ZINC000416363055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416363055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363055 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 14, 39, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 246) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1) `ZINC000416363055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416363055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363055 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 14, 39, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 14, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416363055 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363055 Building ZINC000416363056 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416363056 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/247 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1) `ZINC000416363056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416363056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363056 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 15, 40, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 15, 15, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/248 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1) `ZINC000416363056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416363056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363056 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 14, 39, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416363056 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 Building ZINC000416363056 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000416363056 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 247) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1) `ZINC000416363056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000416363056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363056 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 15, 40, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 15, 15, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 248) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1) `ZINC000416363056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000416363056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000416363056 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2COc2cccnc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 14, 39, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/74215/xan-8058115.14/working/building/ZINC000416363056 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000416363056 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000416363056 Building ZINC000489416837 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489416837 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/249 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC000489416837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489416837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489416837 none COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 2, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 46, 46, 48, 48, 48, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/250 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC000489416837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489416837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489416837 none COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 45, 45, 45, 45, 45, 45, 45, 45, 10, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 45, 45, 47, 47, 47, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 45, 45, 45, 45] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489416837 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 Building ZINC000489416837 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489416837 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 249) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC000489416837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489416837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489416837 none COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 2, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 46, 46, 48, 48, 48, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 250) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC000489416837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489416837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489416837 none COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 45, 45, 45, 45, 45, 45, 45, 45, 10, 2, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 45, 45, 47, 47, 47, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 45, 45, 45, 45] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000489416837 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000489416837 Building ZINC000112027339 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112027339 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/251 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112027339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027339 none Cc1noc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/252 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112027339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027339 none Cc1noc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112027339 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 Building ZINC000112027339 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112027339 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 251) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112027339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027339 none Cc1noc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 252) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112027339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027339 none Cc1noc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112027339 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027339 Building ZINC000112027341 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112027341 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/253 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112027341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027341 none Cc1noc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 25, 25, 25, 25, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/254 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112027341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027341 none Cc1noc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112027341 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 Building ZINC000112027341 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112027341 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 253) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112027341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027341 none Cc1noc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 25, 25, 25, 25, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 254) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1) `ZINC000112027341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112027341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000112027341 none Cc1noc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 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, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112027341 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112027341 Building ZINC000112918711 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112918711 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/255 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000112918711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112918711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000112918711 none O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 9, 9, 9, 9, 25, 26, 26, 26, 26, 9, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 23, 23, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/256 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000112918711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112918711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000112918711 none O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 8, 8, 8, 8, 27, 27, 27, 27, 27, 8, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112918711 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 Building ZINC000112918711 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112918711 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 255) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000112918711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112918711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000112918711 none O=C(N1CCC(CN2CCCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 9, 9, 9, 9, 25, 26, 26, 26, 26, 9, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 23, 23, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 256) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000112918711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112918711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000112918711 none O=C(N1CCC(CN2CCCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 8, 8, 8, 8, 27, 27, 27, 27, 27, 8, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112918711 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112918711 Building ZINC000181457505 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181457505 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/257 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181457505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457505 none CC[C@@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/258 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181457505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457505 none CC[C@@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 50, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 26, 26] 50 rigid atoms, others: [43, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000181457505 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 Building ZINC000181457505 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181457505 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 257) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181457505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457505 none CC[C@@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 258) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181457505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457505 none CC[C@@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 50, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 26, 26] 50 rigid atoms, others: [43, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000181457505 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457505 Building ZINC000181457526 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181457526 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/259 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181457526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457526 none CC[C@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 50, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/260 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181457526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457526 none CC[C@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 28, 28, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000181457526 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 Building ZINC000181457526 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181457526 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 259) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181457526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457526 none CC[C@H](C)Oc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 50, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 260) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000181457526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181457526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181457526 none CC[C@H](C)Oc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 28, 28, 28, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000181457526 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000181457526 Building ZINC000363814814 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000363814814 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/261 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1) `ZINC000363814814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000363814814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000363814814 none Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 28, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 7, 7, 28, 28, 28, 28, 7, 28, 7, 7, 7, 7, 7, 2, 3, 3, 3, 3, 3, 3, 3, 3, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/262 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1) `ZINC000363814814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000363814814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000363814814 none Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 25, 25, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 25, 25, 25, 25, 6, 25, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000363814814 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 Building ZINC000363814814 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000363814814 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 261) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1) `ZINC000363814814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000363814814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000363814814 none Cc1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 28, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 7, 7, 28, 28, 28, 28, 7, 28, 7, 7, 7, 7, 7, 2, 3, 3, 3, 3, 3, 3, 3, 3, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 262) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1) `ZINC000363814814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000363814814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000363814814 none Cc1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 25, 25, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 25, 25, 25, 25, 6, 25, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000363814814 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000363814814 Building ZINC000280711763 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711763 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/263 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711763 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [31, 31, 31, 31, 13, 2, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 32, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/264 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711763 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [34, 34, 34, 34, 12, 2, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 34, 49, 49, 49, 49, 49, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5, 34, 34, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711763 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 Building ZINC000280711763 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711763 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 263) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711763 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [31, 31, 31, 31, 13, 2, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 32, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 264) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711763 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [34, 34, 34, 34, 12, 2, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 34, 49, 49, 49, 49, 49, 34, 34, 34, 34, 34, 34, 5, 5, 10, 5, 5, 34, 34, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711763 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711763 Building ZINC000280711767 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711767 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/265 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711767 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [37, 37, 37, 37, 21, 1, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 37, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 3, 3, 6, 3, 3, 37, 37, 50, 50, 50, 50, 50] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/266 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711767 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [30, 30, 30, 30, 14, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 30, 30, 30, 30, 30, 4, 4, 8, 4, 4, 30, 30, 48, 48, 33, 48, 48] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711767 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 Building ZINC000280711767 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711767 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 265) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711767 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [37, 37, 37, 37, 21, 1, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 37, 37, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 3, 3, 6, 3, 3, 37, 37, 50, 50, 50, 50, 50] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 266) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711767 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [30, 30, 30, 30, 14, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 30, 30, 30, 30, 30, 4, 4, 8, 4, 4, 30, 30, 48, 48, 33, 48, 48] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711767 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711767 Building ZINC000280711772 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711772 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/267 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711772 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [30, 30, 30, 30, 15, 1, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 36, 49, 49, 30, 30, 30, 30, 30, 30, 5, 5, 10, 5, 5, 30, 30, 49, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/268 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711772 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [31, 31, 31, 31, 16, 1, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 36, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31, 49, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711772 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 Building ZINC000280711772 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711772 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 267) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711772 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [30, 30, 30, 30, 15, 1, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 36, 49, 49, 30, 30, 30, 30, 30, 30, 5, 5, 10, 5, 5, 30, 30, 49, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 268) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)O1) `ZINC000280711772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711772 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 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: [31, 31, 31, 31, 16, 1, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 36, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31, 49, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711772 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711772 Building ZINC000280711775 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711775 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/269 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711775 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 13, 1, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 49, 49, 32, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 10, 5, 5, 32, 32, 49, 49, 32, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/270 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711775 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 49, 49, 29, 49, 49, 29, 29, 29, 29, 29, 29, 5, 5, 10, 5, 5, 29, 29, 49, 49, 29, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711775 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 Building ZINC000280711775 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280711775 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 269) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280711775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711775 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 13, 1, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 49, 49, 32, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 10, 5, 5, 32, 32, 49, 49, 32, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 270) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)O1) `ZINC000280711775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280711775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280711775 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 49, 49, 29, 49, 49, 29, 29, 29, 29, 29, 29, 5, 5, 10, 5, 5, 29, 29, 49, 49, 29, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280711775 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280711775 Building ZINC000016970150 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016970150 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/271 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/271' -> `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)NCc1ccc(Cl)cc1Cl) `ZINC000016970150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016970150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016970150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/272 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/272' -> `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)NCc1ccc(Cl)cc1Cl) `ZINC000016970150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016970150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016970150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 40, 40, 24, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000016970150 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 Building ZINC000016970150 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016970150 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 271) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Cl) `ZINC000016970150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016970150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016970150 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 17, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 272) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Cl) `ZINC000016970150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016970150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016970150 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 40, 40, 24, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000016970150 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000016970150 Building ZINC000936395477 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936395477 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/273 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1) `ZINC000936395477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936395477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936395477 none CCN(CC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 12, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 27, 45, 45, 48, 48, 48, 48, 29, 29, 29, 29, 29, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 176 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/274 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1) `ZINC000936395477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936395477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936395477 none CCN(CC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 19, 40, 40, 48, 48, 48, 48, 21, 21, 21, 21, 21, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [45, 43, 37, 38, 7, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936395477 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 Building ZINC000936395477 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936395477 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 273) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1) `ZINC000936395477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936395477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936395477 none CCN(CC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 12, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 27, 45, 45, 48, 48, 48, 48, 29, 29, 29, 29, 29, 12, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [45, 43, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 176 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 274) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1) `ZINC000936395477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936395477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936395477 none CCN(CC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 19, 40, 40, 48, 48, 48, 48, 21, 21, 21, 21, 21, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [45, 43, 37, 38, 7, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936395477 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936395477 Building ZINC000184917378 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184917378 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/275 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1) `ZINC000184917378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184917378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000184917378 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 47, 47, 47, 47, 47, 5, 6, 6, 6, 6, 6, 6, 6, 3, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/276 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1) `ZINC000184917378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184917378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000184917378 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 47, 47, 47, 47, 47, 5, 6, 6, 6, 6, 6, 6, 6, 3, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000184917378 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 Building ZINC000184917378 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184917378 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 275) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1) `ZINC000184917378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184917378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000184917378 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 47, 47, 47, 47, 47, 5, 6, 6, 6, 6, 6, 6, 6, 3, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 276) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1) `ZINC000184917378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184917378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000184917378 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncn(C3CCCCC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 47, 47, 47, 47, 47, 5, 6, 6, 6, 6, 6, 6, 6, 3, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000184917378 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000184917378 Building ZINC000680639728 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680639728 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/277 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl) `ZINC000680639728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680639728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639728 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [12, 6, 2, 6, 6, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 17, 24, 24, 8, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 8, 8, 8, 8, 24, 8, 8, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 106 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/278 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl) `ZINC000680639728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680639728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639728 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [15, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 17, 28, 28, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 28, 6, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680639728 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 Building ZINC000680639728 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680639728 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 277) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl) `ZINC000680639728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680639728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639728 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [12, 6, 2, 6, 6, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 17, 24, 24, 8, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 8, 8, 8, 8, 24, 8, 8, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 106 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 278) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl) `ZINC000680639728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680639728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639728 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [15, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 17, 28, 28, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 28, 6, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680639728 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639728 Building ZINC000680639729 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680639729 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/279 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl) `ZINC000680639729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680639729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639729 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [15, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 16, 27, 27, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 27, 6, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/280 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl) `ZINC000680639729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680639729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639729 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [10, 5, 2, 5, 5, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 18, 25, 25, 8, 5, 5, 5, 10, 10, 10, 5, 5, 8, 8, 8, 8, 8, 8, 25, 8, 8, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680639729 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 Building ZINC000680639729 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680639729 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 279) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl) `ZINC000680639729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680639729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639729 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [15, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 16, 27, 27, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 27, 6, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 280) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl) `ZINC000680639729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680639729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000680639729 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](OC(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', '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, 5, 5, 7, 12, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [10, 5, 2, 5, 5, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 18, 25, 25, 8, 5, 5, 5, 10, 10, 10, 5, 5, 8, 8, 8, 8, 8, 8, 25, 8, 8, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000680639729 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000680639729 Building ZINC000243338187 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243338187 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/281 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1) `ZINC000243338187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243338187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243338187 none COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 30, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 30, 30, 30, 15, 15, 15, 3, 6, 6, 6, 6, 15] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/282 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1) `ZINC000243338187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243338187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243338187 none COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 30, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 30, 30, 30, 15, 15, 15, 3, 5, 5, 5, 5, 15] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243338187 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 Building ZINC000243338187 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243338187 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 281) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1) `ZINC000243338187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243338187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243338187 none COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 30, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 30, 30, 30, 15, 15, 15, 3, 6, 6, 6, 6, 15] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 282) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1) `ZINC000243338187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243338187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243338187 none COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 30, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 30, 30, 30, 15, 15, 15, 3, 5, 5, 5, 5, 15] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243338187 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243338187 Building ZINC000911946401 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911946401 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/283 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911946401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946401 none O=C(N1CCCCC[C@@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 1, 21, 29, 29, 29, 29, 29, 29, 29, 29, 42, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 42, 42, 126, 4, 4, 4] 150 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: 262 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/284 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911946401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946401 none O=C(N1CCCCC[C@@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 1, 23, 28, 28, 28, 28, 28, 28, 28, 28, 47, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 47, 47, 141, 5, 2, 5] 150 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: 307 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911946401 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 Building ZINC000911946401 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911946401 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 283) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911946401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946401 none O=C(N1CCCCC[C@@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 1, 21, 29, 29, 29, 29, 29, 29, 29, 29, 42, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 42, 42, 126, 4, 4, 4] 150 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: 262 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 284) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911946401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946401 none O=C(N1CCCCC[C@@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 1, 23, 28, 28, 28, 28, 28, 28, 28, 28, 47, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 47, 47, 141, 5, 2, 5] 150 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: 307 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911946401 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946401 Building ZINC000911946409 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911946409 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/285 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911946409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946409 none O=C(N1CCCCC[C@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 1, 20, 28, 28, 28, 28, 28, 28, 28, 28, 48, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 144, 5, 1, 5] 150 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: 312 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/286 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911946409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946409 none O=C(N1CCCCC[C@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 1, 15, 21, 21, 21, 21, 21, 21, 21, 21, 43, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 43, 43, 129, 6, 1, 6] 150 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: 297 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911946409 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 Building ZINC000911946409 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911946409 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 285) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911946409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946409 none O=C(N1CCCCC[C@H]1CO)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 1, 20, 28, 28, 28, 28, 28, 28, 28, 28, 48, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48, 144, 5, 1, 5] 150 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: 312 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 286) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCC[C@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000911946409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911946409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000911946409 none O=C(N1CCCCC[C@H]1CO)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 1, 15, 21, 21, 21, 21, 21, 21, 21, 21, 43, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 43, 43, 129, 6, 1, 6] 150 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: 297 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911946409 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911946409 Building ZINC000490001071 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490001071 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/287 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1) `ZINC000490001071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490001071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000490001071 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 27, 27, 27, 27, 27, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 14, 14, 27, 27, 27, 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: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/288 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1) `ZINC000490001071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490001071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000490001071 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 14, 29, 29, 29, 29, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 14, 14, 29, 29, 29, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000490001071 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 Building ZINC000490001071 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490001071 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 287) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1) `ZINC000490001071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490001071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000490001071 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 27, 27, 27, 27, 27, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 14, 14, 27, 27, 27, 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: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 288) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1) `ZINC000490001071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490001071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000490001071 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 14, 29, 29, 29, 29, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 14, 14, 29, 29, 29, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000490001071 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490001071 Building ZINC000153956961 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153956961 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/289 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000153956961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153956961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000153956961 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 30, 30, 30, 10, 10, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/290 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000153956961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153956961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000153956961 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 27, 27, 27, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153956961 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 Building ZINC000153956961 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153956961 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 289) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000153956961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153956961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000153956961 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 30, 30, 30, 10, 10, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 290) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000153956961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153956961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000153956961 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 27, 27, 27, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000153956961 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000153956961 Building ZINC000243360476 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243360476 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/291 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243360476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243360476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000243360476 none COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 29, 29, 29, 29, 29, 20, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 29, 29, 29, 29, 20, 20, 13, 13, 3, 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/292 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243360476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243360476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000243360476 none COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 29, 29, 29, 29, 29, 20, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 29, 29, 29, 29, 20, 20, 13, 13, 3, 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243360476 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 Building ZINC000243360476 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243360476 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 291) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243360476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243360476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000243360476 none COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 29, 29, 29, 29, 29, 20, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 29, 29, 29, 29, 20, 20, 13, 13, 3, 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 292) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243360476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243360476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000243360476 none COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 29, 29, 29, 29, 29, 20, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 29, 29, 29, 29, 20, 20, 13, 13, 3, 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243360476 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243360476 Building ZINC000855796996 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855796996 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/293 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855796996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796996 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 16, 16, 4, 9, 9, 37, 37] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/294 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855796996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796996 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 17, 17, 4, 10, 10, 33, 33] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000855796996 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 Building ZINC000855796996 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855796996 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 293) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855796996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796996 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 16, 16, 4, 9, 9, 37, 37] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 294) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855796996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796996 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 17, 17, 4, 10, 10, 33, 33] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000855796996 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796996 Building ZINC000855796997 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855796997 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/295 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855796997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796997 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 17, 17, 4, 10, 10, 33, 33] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/296 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855796997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796997 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 16, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 10, 10, 36, 36] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000855796997 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 Building ZINC000855796997 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855796997 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 295) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855796997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796997 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 17, 17, 4, 10, 10, 33, 33] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 296) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F) `ZINC000855796997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855796997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000855796997 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 16, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 10, 10, 36, 36] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000855796997 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000855796997 Building ZINC000123007931 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123007931 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/297 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000123007931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123007931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000123007931 none CCNCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 33, 33, 33, 33, 33, 33, 24, 24, 2, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/298 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000123007931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123007931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000123007931 none CCNCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 35, 35, 35, 35, 35, 35, 23, 23, 2, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000123007931 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 Building ZINC000123007931 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123007931 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 297) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000123007931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123007931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000123007931 none CCNCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 33, 33, 33, 33, 33, 33, 24, 24, 2, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 298) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC000123007931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123007931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000123007931 none CCNCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 35, 35, 35, 35, 35, 35, 23, 23, 2, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000123007931 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123007931 Building ZINC000173543548 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173543548 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/299 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1) `ZINC000173543548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173543548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543548 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 2, 14, 14, 20, 20, 20, 20, 20, 20, 20, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 43, 43, 43, 43, 43, 43, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/300 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1) `ZINC000173543548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173543548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543548 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 6, 6, 1, 1, 1, 3, 15, 15, 18, 18, 18, 18, 18, 18, 18, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173543548 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 Building ZINC000173543548 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173543548 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 299) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1) `ZINC000173543548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173543548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543548 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 2, 14, 14, 20, 20, 20, 20, 20, 20, 20, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 43, 43, 43, 43, 43, 43, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 300) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1) `ZINC000173543548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173543548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543548 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 6, 6, 1, 1, 1, 3, 15, 15, 18, 18, 18, 18, 18, 18, 18, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173543548 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543548 Building ZINC000173543562 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173543562 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/301 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1) `ZINC000173543562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173543562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543562 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 13, 13, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/302 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1) `ZINC000173543562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173543562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543562 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 2, 15, 15, 18, 18, 18, 18, 18, 18, 18, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 43, 43, 43, 43, 43, 43, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173543562 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 Building ZINC000173543562 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173543562 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 301) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1) `ZINC000173543562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173543562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543562 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 13, 13, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 302) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1) `ZINC000173543562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173543562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173543562 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2cccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 2, 15, 15, 18, 18, 18, 18, 18, 18, 18, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 43, 43, 43, 43, 43, 43, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173543562 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173543562 Building ZINC000092523246 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000092523246 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/303 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000092523246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523246 none CC(C)(C)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 20, 31, 31, 17, 6, 17, 17, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 33, 33, 99, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 341 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/304 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000092523246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523246 none CC(C)(C)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 32, 32, 18, 6, 18, 18, 35, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 35, 35, 105, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 344 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000092523246 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 Building ZINC000092523246 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000092523246 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 303) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000092523246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523246 none CC(C)(C)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 20, 31, 31, 17, 6, 17, 17, 33, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 33, 33, 99, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 341 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 304) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000092523246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523246 none CC(C)(C)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 32, 32, 18, 6, 18, 18, 35, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 35, 35, 105, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 344 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000092523246 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523246 Building ZINC000092523247 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000092523247 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/305 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000092523247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523247 none CC(C)(C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 21, 29, 29, 17, 6, 17, 17, 35, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 35, 35, 105, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 335 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/306 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000092523247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523247 none CC(C)(C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 20, 25, 25, 15, 6, 15, 15, 35, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 35, 35, 105, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 320 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000092523247 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 Building ZINC000092523247 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000092523247 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 305) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000092523247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523247 none CC(C)(C)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 21, 29, 29, 17, 6, 17, 17, 35, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 35, 35, 105, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 335 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 306) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000092523247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000092523247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000092523247 none CC(C)(C)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 20, 25, 25, 15, 6, 15, 15, 35, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 35, 35, 105, 6, 6, 6, 6, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 320 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000092523247 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000092523247 Building ZINC000154113037 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000154113037 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/307 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000154113037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000154113037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000154113037 none CCC(CC)(CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 14, 28, 39, 29, 39, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 40, 41, 41, 39, 39, 40, 39, 39, 40, 40, 39, 39, 117, 14, 14, 2, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 427 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/308 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000154113037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000154113037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000154113037 none CCC(CC)(CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 30, 14, 30, 39, 30, 40, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 42, 43, 43, 41, 40, 39, 40, 39, 40, 40, 40, 40, 120, 14, 14, 2, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 426 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000154113037 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 Building ZINC000154113037 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000154113037 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 307) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000154113037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000154113037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000154113037 none CCC(CC)(CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 14, 28, 39, 29, 39, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 40, 41, 41, 39, 39, 40, 39, 39, 40, 40, 39, 39, 117, 14, 14, 2, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 427 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 308) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000154113037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000154113037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000154113037 none CCC(CC)(CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 30, 14, 30, 39, 30, 40, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 42, 43, 43, 41, 40, 39, 40, 39, 40, 40, 40, 40, 120, 14, 14, 2, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 426 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000154113037 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154113037 Building ZINC000123077280 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123077280 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/309 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1) `ZINC000123077280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123077280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000123077280 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1 NO_LONG_NAME dock atom 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', 'N.2', 'C.2', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 2, 2, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/310 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1) `ZINC000123077280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123077280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000123077280 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1 NO_LONG_NAME dock atom 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', 'N.2', 'C.2', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 2, 2, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000123077280 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 Building ZINC000123077280 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123077280 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 309) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1) `ZINC000123077280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123077280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000123077280 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1 NO_LONG_NAME dock atom 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', 'N.2', 'C.2', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 2, 2, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 310) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1) `ZINC000123077280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123077280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000123077280 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)c2ccc3nc(C)sc3c2)cn1 NO_LONG_NAME dock atom 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', 'N.2', 'C.2', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 14, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 2, 2, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000123077280 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123077280 Building ZINC000123112617 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123112617 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/311 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1) `ZINC000123112617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123112617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000123112617 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 13, 14, 14, 48, 48, 48, 48, 48, 50, 48, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 14, 14, 14, 14, 14, 14, 48, 48, 48, 50, 50, 50, 48, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/312 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1) `ZINC000123112617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123112617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000123112617 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 14, 13, 14, 48, 48, 48, 48, 48, 50, 48, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 14, 14, 14, 14, 14, 14, 48, 48, 48, 50, 50, 50, 48, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000123112617 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 Building ZINC000123112617 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123112617 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 311) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1) `ZINC000123112617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123112617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000123112617 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 13, 14, 14, 48, 48, 48, 48, 48, 50, 48, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 14, 14, 14, 14, 14, 14, 48, 48, 48, 50, 50, 50, 48, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 312) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1) `ZINC000123112617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123112617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000123112617 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)c2cccc(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 14, 13, 14, 48, 48, 48, 48, 48, 50, 48, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 14, 14, 14, 14, 14, 14, 48, 48, 48, 50, 50, 50, 48, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000123112617 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000123112617 Building ZINC000585246085 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585246085 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/313 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1) `ZINC000585246085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585246085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585246085 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 39, 39, 39, 39, 39, 39, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 39, 39, 39, 39, 39, 39, 4, 4] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/314 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1) `ZINC000585246085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585246085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585246085 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 22, 41, 41, 41, 41, 41, 41, 5, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 41, 41, 41, 41, 41, 41, 5, 5] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585246085 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 Building ZINC000585246085 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585246085 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 313) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1) `ZINC000585246085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585246085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585246085 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 39, 39, 39, 39, 39, 39, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 39, 39, 39, 39, 39, 39, 4, 4] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 314) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1) `ZINC000585246085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585246085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585246085 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC(Oc2cccc(C)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 22, 41, 41, 41, 41, 41, 41, 5, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 41, 41, 41, 41, 41, 41, 5, 5] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585246085 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585246085 Building ZINC000194180465 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194180465 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/315 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1) `ZINC000194180465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194180465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000194180465 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 28, 28, 9, 9, 48, 49, 49, 48, 48, 28, 28, 9, 9, 9, 5, 3, 3, 1, 3, 3, 28, 28, 48, 48, 49, 49, 49, 49, 28, 28] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/316 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1) `ZINC000194180465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194180465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000194180465 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 28, 28, 13, 28, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 5, 3, 3, 1, 3, 3, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194180465 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 Building ZINC000194180465 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194180465 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 315) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1) `ZINC000194180465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194180465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000194180465 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 28, 28, 9, 9, 48, 49, 49, 48, 48, 28, 28, 9, 9, 9, 5, 3, 3, 1, 3, 3, 28, 28, 48, 48, 49, 49, 49, 49, 28, 28] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 316) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1) `ZINC000194180465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194180465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000194180465 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 28, 28, 13, 28, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 5, 3, 3, 1, 3, 3, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000194180465 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000194180465 Building ZINC000585336117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585336117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/317 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585336117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336117 none O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 9, 9, 9, 9, 9, 9, 22, 34, 34, 27, 34, 34, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 34, 34, 34, 34, 9, 9, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/318 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585336117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336117 none O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 9, 9, 9, 9, 9, 26, 38, 38, 30, 38, 38, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 38, 38, 38, 38, 9, 9, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585336117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 Building ZINC000585336117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585336117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 317) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585336117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336117 none O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 9, 9, 9, 9, 9, 9, 22, 34, 34, 27, 34, 34, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 34, 34, 34, 34, 9, 9, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 318) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585336117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336117 none O=C(N1CCC[C@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 9, 9, 9, 9, 9, 26, 38, 38, 30, 38, 38, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 38, 38, 38, 38, 9, 9, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585336117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336117 Building ZINC000585336118 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585336118 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/319 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585336118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336118 none O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 11, 11, 11, 11, 11, 11, 27, 35, 35, 29, 35, 35, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 35, 35, 35, 35, 11, 11, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/320 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585336118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336118 none O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 8, 8, 8, 8, 8, 8, 21, 32, 32, 25, 32, 32, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 8, 8, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585336118 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 Building ZINC000585336118 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585336118 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 319) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585336118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336118 none O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 11, 11, 11, 11, 11, 11, 27, 35, 35, 29, 35, 35, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 35, 35, 35, 35, 11, 11, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 320) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585336118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585336118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000585336118 none O=C(N1CCC[C@@H](Oc2ccncc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 8, 8, 8, 8, 8, 8, 21, 32, 32, 25, 32, 32, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 8, 8, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585336118 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585336118 Building ZINC000585388481 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585388481 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/321 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585388481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585388481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000585388481 none O=C(N1CCOc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/322 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585388481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585388481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000585388481 none O=C(N1CCOc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585388481 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 Building ZINC000585388481 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000585388481 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 321) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585388481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000585388481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000585388481 none O=C(N1CCOc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 322) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000585388481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000585388481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000585388481 none O=C(N1CCOc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000585388481 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000585388481 Building ZINC000490600521 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490600521 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/323 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1) `ZINC000490600521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490600521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000490600521 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 21, 21, 21, 21, 21, 8, 4, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/324 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1) `ZINC000490600521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490600521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000490600521 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 19, 19, 19, 19, 19, 7, 4, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000490600521 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 Building ZINC000490600521 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490600521 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 323) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1) `ZINC000490600521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490600521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000490600521 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 21, 21, 21, 21, 21, 8, 4, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 324) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1) `ZINC000490600521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490600521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000490600521 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c3ccncc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 19, 19, 19, 19, 19, 7, 4, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000490600521 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000490600521 Building ZINC000243403324 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243403324 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/325 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccncc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243403324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243403324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000243403324 none CN(CCc1ccncc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 17, 17, 24, 24, 22, 24, 24, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 24, 24, 24, 24, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/326 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccncc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243403324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243403324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000243403324 none CN(CCc1ccncc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 17, 17, 24, 24, 22, 24, 24, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 24, 24, 24, 24, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243403324 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 Building ZINC000243403324 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243403324 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 325) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccncc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243403324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243403324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000243403324 none CN(CCc1ccncc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 17, 17, 24, 24, 22, 24, 24, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 24, 24, 24, 24, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 326) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccncc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243403324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243403324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000243403324 none CN(CCc1ccncc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 17, 17, 24, 24, 22, 24, 24, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 24, 24, 24, 24, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243403324 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243403324 Building ZINC000110298083 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110298083 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/327 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000110298083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110298083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000110298083 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 10, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 30, 30, 30, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/328 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000110298083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110298083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000110298083 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 7, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 30, 30, 30, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000110298083 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 Building ZINC000110298083 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110298083 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 327) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000110298083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110298083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000110298083 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 10, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 30, 30, 30, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 328) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000110298083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110298083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000110298083 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 7, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 30, 30, 30, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000110298083 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000110298083 Building ZINC000124175215 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124175215 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/329 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000124175215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124175215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000124175215 none CCNCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 9, 9, 9, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 29, 29, 29, 29, 29, 29, 23, 23, 9, 3, 9, 9, 3, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/330 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000124175215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124175215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000124175215 none CCNCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 23, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 30, 30, 29, 23, 23, 8, 8, 8, 8, 2, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124175215 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 Building ZINC000124175215 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124175215 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 329) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000124175215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124175215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000124175215 none CCNCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 9, 9, 9, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 29, 29, 29, 29, 29, 29, 23, 23, 9, 3, 9, 9, 3, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 330) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000124175215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124175215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000124175215 none CCNCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 23, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 30, 30, 29, 23, 23, 8, 8, 8, 8, 2, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124175215 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124175215 Building ZINC000515189704 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515189704 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/331 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)C2)cn1) `ZINC000515189704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515189704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189704 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 15, 15, 15, 15, 15, 22, 22, 17, 22, 22, 15, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 15, 15, 15, 15, 22, 22, 17, 22, 22, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/332 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)C2)cn1) `ZINC000515189704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515189704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189704 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 27, 27, 16, 27, 27, 13, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13, 27, 27, 15, 27, 27, 13, 13, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000515189704 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 Building ZINC000515189704 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515189704 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 331) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)C2)cn1) `ZINC000515189704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515189704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189704 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 15, 15, 15, 15, 15, 22, 22, 17, 22, 22, 15, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 15, 15, 15, 15, 22, 22, 17, 22, 22, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 332) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)C2)cn1) `ZINC000515189704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515189704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189704 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 27, 27, 16, 27, 27, 13, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 13, 13, 27, 27, 15, 27, 27, 13, 13, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000515189704 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189704 Building ZINC000515189705 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515189705 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/333 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)C2)cn1) `ZINC000515189705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515189705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189705 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 12, 12, 12, 21, 21, 16, 21, 21, 12, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 12, 12, 12, 12, 21, 21, 18, 21, 21, 12, 12, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/334 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)C2)cn1) `ZINC000515189705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515189705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189705 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 15, 15, 15, 15, 15, 27, 27, 19, 27, 27, 15, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 15, 15, 15, 15, 27, 27, 23, 27, 27, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000515189705 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 Building ZINC000515189705 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515189705 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 333) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)C2)cn1) `ZINC000515189705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515189705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189705 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 12, 12, 12, 21, 21, 16, 21, 21, 12, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 12, 12, 12, 12, 21, 21, 18, 21, 21, 12, 12, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 334) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)C2)cn1) `ZINC000515189705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515189705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000515189705 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](F)(c3ccccc3)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', 'F', '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', '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, 15, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 15, 15, 15, 15, 15, 27, 27, 19, 27, 27, 15, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 15, 15, 15, 15, 27, 27, 23, 27, 27, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000515189705 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000515189705 Building ZINC000124462545 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124462545 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/335 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1) `ZINC000124462545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124462545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000124462545 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 12, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 10, 6, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/336 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1) `ZINC000124462545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124462545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000124462545 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 12, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 10, 6, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124462545 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 Building ZINC000124462545 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124462545 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 335) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1) `ZINC000124462545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124462545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000124462545 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 12, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 10, 6, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 336) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1) `ZINC000124462545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124462545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000124462545 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3oc(C)c(C)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 12, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 10, 6, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124462545 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124462545 Building ZINC000124679927 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124679927 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/337 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1) `ZINC000124679927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124679927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124679927 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 18, 23, 32, 6, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 4, 18, 18, 23, 23, 32, 32, 96, 11, 11, 11, 11, 11, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 277 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/338 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1) `ZINC000124679927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124679927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124679927 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 17, 22, 30, 6, 12, 12, 6, 12, 12, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 22, 22, 30, 30, 90, 12, 12, 6, 12, 12, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124679927 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 Building ZINC000124679927 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124679927 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 337) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1) `ZINC000124679927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124679927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124679927 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 18, 23, 32, 6, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 4, 18, 18, 23, 23, 32, 32, 96, 11, 11, 11, 11, 11, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 277 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 338) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1) `ZINC000124679927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124679927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124679927 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 17, 22, 30, 6, 12, 12, 6, 12, 12, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 22, 22, 30, 30, 90, 12, 12, 6, 12, 12, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124679927 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124679927 Building ZINC000124680153 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124680153 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/339 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1) `ZINC000124680153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124680153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124680153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 17, 22, 30, 6, 12, 12, 6, 12, 12, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 22, 22, 30, 30, 90, 12, 12, 6, 12, 12, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/340 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1) `ZINC000124680153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124680153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124680153 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 17, 22, 32, 6, 11, 11, 6, 11, 11, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 22, 22, 32, 32, 96, 11, 11, 6, 11, 11, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124680153 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 Building ZINC000124680153 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124680153 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 339) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1) `ZINC000124680153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124680153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124680153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 17, 22, 30, 6, 12, 12, 6, 12, 12, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 22, 22, 30, 30, 90, 12, 12, 6, 12, 12, 6, 6] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 340) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1) `ZINC000124680153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124680153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000124680153 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CCCO)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 17, 22, 32, 6, 11, 11, 6, 11, 11, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 22, 22, 32, 32, 96, 11, 11, 6, 11, 11, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 295 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124680153 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124680153 Building ZINC001125991589 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001125991589 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/341 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1) `ZINC001125991589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001125991589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001125991589 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 29, 29, 29, 29, 29, 7, 7, 7, 5, 5, 29, 29, 29, 29] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/342 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1) `ZINC001125991589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001125991589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001125991589 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 29, 29, 29, 29, 29, 7, 7, 7, 6, 6, 29, 29, 29, 29] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001125991589 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 Building ZINC001125991589 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001125991589 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 341) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1) `ZINC001125991589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001125991589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001125991589 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 29, 29, 29, 29, 29, 7, 7, 7, 5, 5, 29, 29, 29, 29] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 342) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1) `ZINC001125991589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001125991589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001125991589 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 29, 29, 29, 29, 29, 7, 7, 7, 6, 6, 29, 29, 29, 29] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001125991589 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001125991589 Building ZINC000154669075 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000154669075 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/343 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C) `ZINC000154669075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000154669075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669075 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/344 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C) `ZINC000154669075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000154669075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669075 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000154669075 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 Building ZINC000154669075 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000154669075 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 343) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C) `ZINC000154669075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000154669075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669075 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 344) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C) `ZINC000154669075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000154669075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669075 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000154669075 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669075 Building ZINC000154669170 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000154669170 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/345 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C) `ZINC000154669170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000154669170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669170 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/346 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C) `ZINC000154669170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000154669170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669170 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000154669170 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 Building ZINC000154669170 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000154669170 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 345) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C) `ZINC000154669170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000154669170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669170 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 346) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C) `ZINC000154669170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000154669170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000154669170 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H]1CCCc2c1cnn2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000154669170 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000154669170 Building ZINC000125204276 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125204276 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/347 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000125204276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125204276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000125204276 none CCC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 20, 20, 20, 11, 9, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 11, 11, 47, 47, 47, 47, 47, 20, 11, 11, 3, 3, 3, 6, 6, 6, 3, 3, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/348 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000125204276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125204276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000125204276 none CCC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 20, 20, 20, 9, 5, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 11, 11, 47, 47, 47, 47, 47, 20, 11, 11, 3, 3, 3, 6, 6, 6, 3, 3, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125204276 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 Building ZINC000125204276 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125204276 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 347) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000125204276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125204276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000125204276 none CCC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 20, 20, 20, 11, 9, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 11, 11, 47, 47, 47, 47, 47, 20, 11, 11, 3, 3, 3, 6, 6, 6, 3, 3, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 348) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000125204276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125204276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000125204276 none CCC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 20, 20, 20, 9, 5, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 11, 11, 47, 47, 47, 47, 47, 20, 11, 11, 3, 3, 3, 6, 6, 6, 3, 3, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125204276 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125204276 Building ZINC000173598074 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173598074 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/349 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173598074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598074 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 50, 50, 25, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/350 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173598074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598074 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173598074 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 Building ZINC000173598074 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173598074 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 349) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173598074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598074 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 50, 50, 25, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 350) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173598074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598074 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173598074 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598074 Building ZINC000173598084 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173598084 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/351 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173598084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598084 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 50, 50, 25, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/352 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173598084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598084 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173598084 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 Building ZINC000173598084 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173598084 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 351) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173598084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598084 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 50, 50, 25, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 352) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1) `ZINC000173598084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173598084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173598084 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2noc(C(C)C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 1, 5, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 50, 50, 28, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173598084 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173598084 Building ZINC000125363191 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125363191 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/353 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1) `ZINC000125363191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125363191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125363191 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 30, 48, 48, 40, 48, 48, 7, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 30, 30, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/354 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1) `ZINC000125363191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125363191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125363191 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 31, 48, 48, 48, 48, 48, 7, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 31, 31, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125363191 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 Building ZINC000125363191 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125363191 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 353) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1) `ZINC000125363191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125363191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125363191 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 30, 48, 48, 40, 48, 48, 7, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 30, 30, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 354) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1) `ZINC000125363191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125363191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125363191 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 31, 48, 48, 48, 48, 48, 7, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 31, 31, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125363191 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125363191 Building ZINC000125395291 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125395291 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/355 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1) `ZINC000125395291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125395291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125395291 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/356 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1) `ZINC000125395291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125395291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125395291 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125395291 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 Building ZINC000125395291 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125395291 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 355) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1) `ZINC000125395291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125395291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125395291 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 356) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1) `ZINC000125395291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125395291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000125395291 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3nccn3C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 39, 39, 39, 39, 39, 18, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125395291 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125395291 Building ZINC000155077851 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155077851 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/357 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155077851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077851 none C[C@@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 11, 23, 23, 32, 32, 32, 32, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 32, 32, 32, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/358 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155077851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077851 none C[C@@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 13, 23, 23, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 13, 13, 31, 31, 31, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155077851 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 Building ZINC000155077851 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155077851 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 357) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155077851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077851 none C[C@@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 11, 23, 23, 32, 32, 32, 32, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 32, 32, 32, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 358) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155077851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077851 none C[C@@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 13, 23, 23, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 13, 13, 31, 31, 31, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155077851 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077851 Building ZINC000155077962 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155077962 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/359 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155077962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077962 none C[C@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 13, 23, 23, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 13, 13, 31, 31, 31, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/360 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155077962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077962 none C[C@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 24, 24, 33, 33, 33, 33, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 12, 12, 33, 33, 33, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155077962 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 Building ZINC000155077962 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155077962 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 359) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155077962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077962 none C[C@H](CC(=O)c1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 13, 23, 23, 31, 31, 31, 31, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 13, 13, 31, 31, 31, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 360) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155077962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155077962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000155077962 none C[C@H](CC(=O)c1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 24, 24, 33, 33, 33, 33, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 12, 12, 33, 33, 33, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155077962 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155077962 Building ZINC000125455802 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125455802 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/361 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1) `ZINC000125455802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125455802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000125455802 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 8, 12, 30, 30, 30, 45, 45, 12, 12, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 30, 43, 45, 45, 45, 45, 45, 45, 12, 12, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/362 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1) `ZINC000125455802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125455802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000125455802 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 4, 8, 30, 30, 30, 45, 45, 12, 12, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 30, 43, 45, 45, 45, 45, 45, 45, 12, 12, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125455802 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 Building ZINC000125455802 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125455802 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 361) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1) `ZINC000125455802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125455802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000125455802 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 8, 12, 30, 30, 30, 45, 45, 12, 12, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 30, 43, 45, 45, 45, 45, 45, 45, 12, 12, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 362) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1) `ZINC000125455802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125455802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000125455802 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(=O)NC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 4, 8, 30, 30, 30, 45, 45, 12, 12, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 30, 43, 45, 45, 45, 45, 45, 45, 12, 12, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125455802 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125455802 Building ZINC000004852021 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000004852021 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/363 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1oc2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000004852021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000004852021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000004852021 none NC(=O)c1oc2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 19, 19, 19, 19, 6, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/364 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1oc2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000004852021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000004852021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000004852021 none NC(=O)c1oc2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 19, 19, 19, 19, 6, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000004852021 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 Building ZINC000004852021 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000004852021 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 363) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1oc2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000004852021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000004852021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000004852021 none NC(=O)c1oc2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 19, 19, 19, 19, 6, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 364) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1oc2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21) `ZINC000004852021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000004852021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000004852021 none NC(=O)c1oc2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 19, 19, 19, 19, 6, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000004852021 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000004852021 Building ZINC000243431873 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243431873 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/365 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1) `ZINC000243431873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243431873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243431873 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 29, 29, 21, 29, 29, 29, 6, 6, 7, 7, 7, 6, 6, 6, 3, 21, 21, 29, 29, 29, 29, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/366 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1) `ZINC000243431873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243431873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243431873 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 29, 29, 21, 29, 29, 29, 6, 6, 7, 7, 7, 6, 6, 6, 3, 21, 21, 29, 29, 29, 29, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243431873 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 Building ZINC000243431873 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243431873 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 365) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1) `ZINC000243431873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243431873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243431873 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 29, 29, 21, 29, 29, 29, 6, 6, 7, 7, 7, 6, 6, 6, 3, 21, 21, 29, 29, 29, 29, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 366) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1) `ZINC000243431873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243431873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243431873 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 29, 29, 21, 29, 29, 29, 6, 6, 7, 7, 7, 6, 6, 6, 3, 21, 21, 29, 29, 29, 29, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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/74215/xan-8058115.14/working/building/ZINC000243431873 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243431873 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243431873 Building ZINC000516988681 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516988681 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/367 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1) `ZINC000516988681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516988681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000516988681 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1 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.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 23, 23, 15, 23, 47, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 15, 15, 23, 23, 23, 23, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/368 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1) `ZINC000516988681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516988681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000516988681 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1 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.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 15, 23, 15, 23, 47, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 15, 15, 23, 23, 15, 23, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000516988681 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 Building ZINC000516988681 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516988681 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 367) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1) `ZINC000516988681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516988681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000516988681 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1 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.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 23, 23, 15, 23, 47, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 15, 15, 23, 23, 23, 23, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 368) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1) `ZINC000516988681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516988681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000516988681 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCCC1 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.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 15, 23, 15, 23, 47, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 15, 15, 23, 23, 15, 23, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000516988681 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000516988681 Building ZINC000280829451 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280829451 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/369 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280829451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829451 none COc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 49, 49, 46, 49, 49, 27, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 49, 49, 49, 49, 27, 27, 14, 14, 14, 14, 14, 14, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/370 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280829451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829451 none COc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 44, 48, 48, 24, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 48, 48, 48, 48, 24, 24, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280829451 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 Building ZINC000280829451 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280829451 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 369) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280829451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829451 none COc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 49, 49, 46, 49, 49, 27, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 49, 49, 49, 49, 27, 27, 14, 14, 14, 14, 14, 14, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 370) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280829451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829451 none COc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 48, 48, 44, 48, 48, 24, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 48, 48, 48, 48, 24, 24, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280829451 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829451 Building ZINC000280829454 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280829454 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/371 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280829454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829454 none COc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 49, 49, 46, 49, 49, 25, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 49, 49, 49, 49, 25, 25, 11, 11, 11, 11, 11, 11, 2, 2, 4, 2, 2] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/372 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280829454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829454 none COc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 49, 49, 43, 49, 49, 25, 13, 13, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 49, 49, 49, 49, 25, 25, 13, 13, 13, 13, 13, 13, 2, 2, 4, 2, 2] 100 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280829454 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 Building ZINC000280829454 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280829454 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 371) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280829454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829454 none COc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 49, 49, 46, 49, 49, 25, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 49, 49, 49, 49, 25, 25, 11, 11, 11, 11, 11, 11, 2, 2, 4, 2, 2] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 372) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280829454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280829454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000280829454 none COc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 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, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 49, 49, 43, 49, 49, 25, 13, 13, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 49, 49, 49, 49, 25, 25, 13, 13, 13, 13, 13, 13, 2, 2, 4, 2, 2] 100 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280829454 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280829454 Building ZINC000243493226 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243493226 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/373 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243493226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243493226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243493226 none COc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 30, 30, 23, 30, 29, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 30, 30, 30, 30, 14, 14, 3, 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, 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/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/374 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243493226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243493226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243493226 none COc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 30, 30, 30, 30, 30, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 30, 30, 30, 30, 14, 14, 3, 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, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243493226 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 Building ZINC000243493226 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243493226 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 373) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243493226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243493226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243493226 none COc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 30, 30, 23, 30, 29, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 30, 30, 30, 30, 14, 14, 3, 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, 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/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 374) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000243493226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243493226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000243493226 none COc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 30, 30, 30, 30, 30, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 30, 30, 30, 30, 14, 14, 3, 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, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243493226 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243493226 Building ZINC000155551364 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155551364 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/375 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155551364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551364 none CC1(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 11, 37, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/376 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155551364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551364 none CC1(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 12, 41, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 41, 41, 41, 41] 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: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155551364 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 Building ZINC000155551364 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155551364 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 375) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155551364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551364 none CC1(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 11, 37, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 376) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155551364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551364 none CC1(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 12, 41, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 41, 41, 41, 41] 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: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155551364 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551364 Building ZINC000155551481 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155551481 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/377 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155551481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551481 none CC1(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 13, 40, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 40, 40, 40, 40] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/378 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155551481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551481 none CC1(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 10, 37, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155551481 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 Building ZINC000155551481 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155551481 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 377) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155551481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551481 none CC1(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 13, 40, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 40, 40, 40, 40] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 378) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000155551481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155551481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000155551481 none CC1(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 10, 37, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 37, 37, 37, 37] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155551481 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155551481 Building ZINC000155660127 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155660127 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/379 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155660127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660127 none O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 20, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 78, 26, 26, 26, 26, 26, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/380 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155660127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660127 none O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 23, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 93, 31, 31, 31, 31, 31, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155660127 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 Building ZINC000155660127 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155660127 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 379) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155660127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660127 none O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 20, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 78, 26, 26, 26, 26, 26, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 380) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155660127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660127 none O=C(NCC1([C@@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 15, 23, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 93, 31, 31, 31, 31, 31, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155660127 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660127 Building ZINC000155660240 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155660240 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/381 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155660240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660240 none O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 18, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 84, 28, 28, 28, 28, 28, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/382 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155660240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660240 none O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 28, 28, 28, 28, 28, 28, 28, 28, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 84, 28, 28, 28, 28, 28, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155660240 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 Building ZINC000155660240 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155660240 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 381) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155660240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660240 none O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 18, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 84, 28, 28, 28, 28, 28, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 382) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000155660240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155660240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155660240 none O=C(NCC1([C@H](O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 28, 28, 28, 28, 28, 28, 28, 28, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 84, 28, 28, 28, 28, 28, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155660240 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155660240 Building ZINC000517525063 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517525063 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/383 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(O)c2ccccc2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517525063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517525063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000517525063 none O=C(Nc1nc(O)c2ccccc2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 9, 15, 15, 15, 12, 15, 15, 15, 15, 15, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 30, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/384 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(O)c2ccccc2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517525063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517525063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000517525063 none O=C(Nc1nc(O)c2ccccc2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 17, 17, 17, 11, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 34, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000517525063 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 Building ZINC000517525063 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517525063 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 383) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(O)c2ccccc2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517525063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517525063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000517525063 none O=C(Nc1nc(O)c2ccccc2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 9, 15, 15, 15, 12, 15, 15, 15, 15, 15, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 30, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 384) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(O)c2ccccc2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517525063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517525063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000517525063 none O=C(Nc1nc(O)c2ccccc2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 17, 17, 17, 11, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 34, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000517525063 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000517525063 Building ZINC000243561309 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243561309 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/385 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1) `ZINC000243561309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243561309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243561309 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 33, 33, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 17, 17, 3, 4, 4, 4, 4, 33, 33] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/386 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1) `ZINC000243561309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243561309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243561309 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 17, 34, 34, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34, 34, 17, 17, 3, 4, 4, 4, 4, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243561309 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 Building ZINC000243561309 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243561309 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 385) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1) `ZINC000243561309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243561309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243561309 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 33, 33, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 17, 17, 3, 4, 4, 4, 4, 33, 33] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 386) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1) `ZINC000243561309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243561309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243561309 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(F)cc32)cc1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 17, 34, 34, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34, 34, 17, 17, 3, 4, 4, 4, 4, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243561309 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243561309 Building ZINC000155744074 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155744074 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/387 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cn1) `ZINC000155744074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155744074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000155744074 none CCc1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 22, 21, 28, 28, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 28, 28, 43, 43, 43, 43, 43, 28, 8, 6, 6, 6, 6, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/388 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cn1) `ZINC000155744074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155744074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000155744074 none CCc1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 28, 21, 28, 28, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 28, 28, 43, 43, 43, 43, 43, 28, 8, 6, 6, 6, 6, 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155744074 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 Building ZINC000155744074 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155744074 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 387) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cn1) `ZINC000155744074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155744074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000155744074 none CCc1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 22, 21, 28, 28, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 28, 28, 43, 43, 43, 43, 43, 28, 8, 6, 6, 6, 6, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 388) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cn1) `ZINC000155744074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155744074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000155744074 none CCc1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 28, 21, 28, 28, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 28, 28, 43, 43, 43, 43, 43, 28, 8, 6, 6, 6, 6, 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155744074 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155744074 Building ZINC000243783333 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243783333 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/389 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1) `ZINC000243783333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243783333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243783333 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 7, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 9, 9, 9, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/390 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1) `ZINC000243783333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243783333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243783333 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 9, 9, 9, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243783333 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 Building ZINC000243783333 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000243783333 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 389) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1) `ZINC000243783333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000243783333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243783333 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 7, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 9, 9, 9, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 390) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1) `ZINC000243783333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000243783333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000243783333 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCc4ccccc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 9, 9, 9, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000243783333 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000243783333 Building ZINC000913726917 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913726917 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/391 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC000913726917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913726917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913726917 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 7, 1, 1, 1, 4, 4, 4, 11, 20, 20, 20, 11, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/392 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC000913726917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913726917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913726917 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 7, 1, 1, 1, 4, 4, 4, 11, 20, 20, 20, 11, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000913726917 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 Building ZINC000913726917 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913726917 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 391) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC000913726917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913726917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913726917 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 7, 1, 1, 1, 4, 4, 4, 11, 20, 20, 20, 11, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 392) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC000913726917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913726917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000913726917 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 7, 1, 1, 1, 4, 4, 4, 11, 20, 20, 20, 11, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000913726917 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000913726917 Building ZINC000336942585 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336942585 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/393 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2oc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000336942585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336942585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000336942585 none Cc1cccc2oc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', '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, 1, 12, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 2, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/394 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2oc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000336942585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336942585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000336942585 none Cc1cccc2oc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', '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, 1, 12, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 2, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000336942585 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 Building ZINC000336942585 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000336942585 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 393) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2oc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000336942585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000336942585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000336942585 none Cc1cccc2oc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', '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, 1, 12, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 2, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 394) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2oc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000336942585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000336942585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000336942585 none Cc1cccc2oc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', '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, 1, 12, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 14, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 10, 10, 2, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000336942585 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000336942585 Building ZINC000244035284 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244035284 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/395 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244035284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244035284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244035284 none COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 31, 31, 31, 15, 15, 15, 3, 4, 4, 4, 4, 4, 4, 4, 4, 15] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/396 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244035284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244035284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244035284 none COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 31, 31, 31, 15, 15, 15, 3, 4, 4, 4, 4, 4, 4, 4, 4, 15] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244035284 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 Building ZINC000244035284 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244035284 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 395) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244035284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244035284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244035284 none COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 31, 31, 31, 15, 15, 15, 3, 4, 4, 4, 4, 4, 4, 4, 4, 15] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 396) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244035284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244035284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244035284 none COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 31, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 31, 31, 31, 15, 15, 15, 3, 4, 4, 4, 4, 4, 4, 4, 4, 15] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244035284 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244035284 Building ZINC000244038622 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244038622 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/397 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1) `ZINC000244038622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244038622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000244038622 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 20, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 7, 7, 3, 20, 20, 27, 27, 27, 27, 27, 27, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/398 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1) `ZINC000244038622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244038622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000244038622 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 19, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 3, 19, 19, 26, 26, 26, 26, 26, 26, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244038622 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 Building ZINC000244038622 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244038622 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 397) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1) `ZINC000244038622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244038622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000244038622 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 20, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 7, 7, 3, 20, 20, 27, 27, 27, 27, 27, 27, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 398) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1) `ZINC000244038622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244038622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000244038622 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCc3ccc(F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 19, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 3, 19, 19, 26, 26, 26, 26, 26, 26, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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/74215/xan-8058115.14/working/building/ZINC000244038622 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244038622 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244038622 Building ZINC000244054018 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244054018 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/399 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244054018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244054018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244054018 none COC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 10, 10, 10, 10, 5, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/400 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244054018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244054018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244054018 none COC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 10, 10, 10, 10, 5, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244054018 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 Building ZINC000244054018 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244054018 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 399) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244054018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244054018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244054018 none COC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 10, 10, 10, 10, 5, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 400) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244054018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244054018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244054018 none COC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 10, 10, 10, 10, 5, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244054018 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244054018 Building ZINC000244185756 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244185756 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/401 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244185756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244185756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244185756 none COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 22, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 31, 31, 31, 31, 22, 22, 14, 14, 3, 4, 4, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/402 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244185756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244185756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244185756 none COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 23, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 31, 31, 31, 31, 23, 23, 14, 14, 3, 4, 4, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244185756 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 Building ZINC000244185756 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244185756 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 401) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244185756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244185756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244185756 none COc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 22, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 31, 31, 31, 31, 22, 22, 14, 14, 3, 4, 4, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 402) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12) `ZINC000244185756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244185756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244185756 none COc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cn(C)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 31, 23, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 31, 31, 31, 31, 23, 23, 14, 14, 3, 4, 4, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244185756 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244185756 Building ZINC000244203640 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244203640 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/403 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc32)c1) `ZINC000244203640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244203640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244203640 none CC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 28, 28, 28, 28, 16, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 5, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/404 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc32)c1) `ZINC000244203640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244203640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244203640 none CC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 28, 28, 28, 28, 16, 16, 16, 3, 4, 4, 4, 4, 4, 4, 4, 4, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244203640 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 Building ZINC000244203640 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244203640 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 403) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc32)c1) `ZINC000244203640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244203640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244203640 none CC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 28, 28, 28, 28, 16, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 5, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 404) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc32)c1) `ZINC000244203640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244203640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000244203640 none CC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 28, 28, 28, 28, 16, 16, 16, 3, 4, 4, 4, 4, 4, 4, 4, 4, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244203640 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244203640 Building ZINC000093049244 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000093049244 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/405 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/405' -> `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)c1ccc(Cl)s1) `ZINC000093049244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000093049244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000093049244 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 13, 13, 13, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/406 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/406' -> `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)c1ccc(Cl)s1) `ZINC000093049244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000093049244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000093049244 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 12, 12, 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]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000093049244 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 Building ZINC000093049244 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000093049244 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 405) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(Cl)s1) `ZINC000093049244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000093049244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000093049244 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 13, 13, 13, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 406) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(Cl)s1) `ZINC000093049244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000093049244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000093049244 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 12, 12, 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]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000093049244 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000093049244 Building ZINC000244254349 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244254349 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/407 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000244254349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244254349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244254349 none O=C(NCc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 32, 32, 32, 32, 32, 4, 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, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/408 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000244254349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244254349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244254349 none O=C(NCc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 28, 28, 28, 28, 28, 4, 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, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244254349 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 Building ZINC000244254349 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244254349 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 407) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000244254349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244254349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244254349 none O=C(NCc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 32, 32, 32, 32, 32, 4, 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, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 408) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21) `ZINC000244254349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244254349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000244254349 none O=C(NCc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 28, 28, 28, 28, 28, 4, 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, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244254349 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244254349 Building ZINC000244335530 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244335530 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/409 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1) `ZINC000244335530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244335530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000244335530 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 20, 20, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 29, 29, 29, 20, 20, 4, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/410 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1) `ZINC000244335530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244335530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000244335530 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 4, 28, 4, 20, 20, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 28, 28, 28, 20, 20, 4, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244335530 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 Building ZINC000244335530 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244335530 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 409) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1) `ZINC000244335530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244335530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000244335530 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 20, 20, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 29, 29, 29, 20, 20, 4, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 410) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1) `ZINC000244335530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244335530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000244335530 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 26, 4, 28, 4, 20, 20, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 28, 28, 28, 20, 20, 4, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244335530 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244335530 Building ZINC000244332030 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244332030 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/411 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21) `ZINC000244332030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244332030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000244332030 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21 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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 21, 28, 28, 28, 21, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/412 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21) `ZINC000244332030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244332030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000244332030 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21 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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 21, 28, 28, 28, 21, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244332030 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 Building ZINC000244332030 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244332030 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 411) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21) `ZINC000244332030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244332030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000244332030 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21 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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 21, 28, 28, 28, 21, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 412) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21) `ZINC000244332030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244332030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000244332030 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)OCCO3)c2ccccc21 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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 21, 28, 28, 28, 21, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244332030 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244332030 Building ZINC000421236138 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236138 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/413 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236138 none C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 6, 6, 6, 6, 21, 21, 23, 23, 23, 23, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 2, 2, 2, 2, 6, 6] 23 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/414 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236138 none C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 10, 10] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236138 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 Building ZINC000421236138 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236138 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 413) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236138 none C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 6, 6, 6, 6, 21, 21, 23, 23, 23, 23, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 2, 2, 2, 2, 6, 6] 23 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 414) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236138 none C[C@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 10, 10] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236138 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236138 Building ZINC000421236140 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236140 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/415 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236140 none C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 44, 44, 50, 50, 50, 50, 13, 6, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/416 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236140 none C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 36, 36, 50, 50, 50, 50, 7, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 7, 7] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236140 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 Building ZINC000421236140 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236140 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 415) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236140 none C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 44, 44, 50, 50, 50, 50, 13, 6, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 416) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236140 none C[C@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 36, 36, 50, 50, 50, 50, 7, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 7, 7] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236140 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236140 Building ZINC000421236143 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236143 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/417 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236143 none C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 39, 39, 50, 50, 50, 50, 8, 5, 2, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/418 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236143 none C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 42, 42, 50, 50, 50, 50, 10, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236143 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 Building ZINC000421236143 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236143 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 417) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236143 none C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 39, 39, 50, 50, 50, 50, 8, 5, 2, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 418) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236143 none C[C@@H]1C[C@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 42, 42, 50, 50, 50, 50, 10, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236143 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236143 Building ZINC000421236145 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236145 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/419 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236145 none C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 40, 40, 50, 50, 50, 50, 9, 6, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/420 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236145 none C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 45, 45, 50, 50, 50, 50, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236145 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 Building ZINC000421236145 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421236145 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 419) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421236145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236145 none C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 40, 40, 50, 50, 50, 50, 9, 6, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 2, 2, 2, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 420) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000421236145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421236145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421236145 none C[C@@H]1C[C@@H](C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 45, 45, 50, 50, 50, 50, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421236145 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421236145 Building ZINC000155968794 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155968794 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/421 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155968794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968794 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 43, 43, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/422 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155968794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968794 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 40, 40, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155968794 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 Building ZINC000155968794 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155968794 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 421) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155968794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968794 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 43, 43, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 422) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155968794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968794 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 40, 40, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155968794 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968794 Building ZINC000155968883 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155968883 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/423 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155968883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968883 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 41, 41, 49, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/424 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155968883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968883 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 39, 39, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155968883 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 Building ZINC000155968883 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000155968883 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 423) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000155968883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968883 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 41, 41, 49, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 424) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(C)C)cc1) `ZINC000155968883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000155968883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000155968883 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2C(=O)OC(C)(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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 39, 39, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000155968883 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000155968883 Building ZINC000244406803 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244406803 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/425 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244406803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244406803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000244406803 none COc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 28, 28, 28, 28, 18, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 31, 31, 31, 28, 28, 28, 18, 18, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/426 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244406803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244406803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000244406803 none COc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 28, 28, 28, 28, 18, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 31, 31, 31, 28, 28, 28, 18, 18, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244406803 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 Building ZINC000244406803 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000244406803 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 425) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244406803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000244406803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000244406803 none COc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 28, 28, 28, 28, 18, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 31, 31, 31, 28, 28, 28, 18, 18, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 426) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1) `ZINC000244406803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000244406803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000244406803 none COc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2cn(C)c3ccccc23)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 28, 28, 28, 28, 18, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 31, 31, 31, 28, 28, 28, 18, 18, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000244406803 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000244406803 Building ZINC001126191909 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001126191909 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/427 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126191909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001126191909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001126191909 none CC(C)(C)OC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 44, 44, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 15, 3, 3, 1, 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, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/428 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126191909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001126191909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001126191909 none CC(C)(C)OC(=O)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 44, 47, 47, 25, 15, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 3, 3, 1, 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, 35]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001126191909 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 Building ZINC001126191909 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001126191909 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 427) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126191909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001126191909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001126191909 none CC(C)(C)OC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 44, 44, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 15, 3, 3, 1, 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, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 428) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001126191909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001126191909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001126191909 none CC(C)(C)OC(=O)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 44, 47, 47, 25, 15, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 3, 3, 1, 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, 35]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001126191909 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001126191909 Building ZINC000046693152 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046693152 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/429 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1) `ZINC000046693152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046693152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000046693152 none COc1cc(OC)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 16, 16, 30, 30, 30, 40, 16, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 39, 30, 39, 39, 35, 30, 40, 40, 40, 16, 16, 5, 4, 4, 4, 4, 4, 4, 4, 39, 39, 39, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/430 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1) `ZINC000046693152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046693152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000046693152 none COc1cc(OC)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 15, 15, 31, 31, 31, 43, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 37, 31, 38, 37, 34, 31, 43, 43, 43, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000046693152 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 Building ZINC000046693152 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046693152 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 429) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1) `ZINC000046693152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046693152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000046693152 none COc1cc(OC)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 16, 16, 30, 30, 30, 40, 16, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 39, 30, 39, 39, 35, 30, 40, 40, 40, 16, 16, 5, 4, 4, 4, 4, 4, 4, 4, 39, 39, 39, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 430) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1) `ZINC000046693152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046693152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000046693152 none COc1cc(OC)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 15, 15, 31, 31, 31, 43, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 37, 31, 38, 37, 34, 31, 43, 43, 43, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000046693152 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000046693152 Building ZINC000421635417 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635417 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/431 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635417 none C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 35, 35, 35, 35, 7, 6, 3, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 2, 2, 2, 2] 35 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/432 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635417 none C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 50, 50, 50, 50, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635417 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 Building ZINC000421635417 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635417 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 431) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635417 none C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 35, 35, 35, 35, 7, 6, 3, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 2, 2, 2, 2] 35 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 432) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635417 none C[C@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 50, 50, 50, 50, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635417 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635417 Building ZINC000421635418 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635418 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/433 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635418 none C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 36, 36, 50, 50, 50, 50, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/434 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635418 none C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 40, 40, 47, 47, 47, 47, 8, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 8, 8, 3, 3, 3, 3] 47 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635418 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 Building ZINC000421635418 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635418 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 433) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635418 none C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 36, 36, 50, 50, 50, 50, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 434) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635418 none C[C@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 40, 40, 47, 47, 47, 47, 8, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 8, 8, 3, 3, 3, 3] 47 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635418 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635418 Building ZINC000421635419 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635419 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/435 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635419 none C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 50, 50, 50, 50, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/436 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635419 none C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 36, 36, 50, 50, 50, 50, 7, 4, 2, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635419 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 Building ZINC000421635419 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635419 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 435) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635419 none C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 50, 50, 50, 50, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 436) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635419 none C[C@@H]1CC[C@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 36, 36, 50, 50, 50, 50, 7, 4, 2, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635419 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635419 Building ZINC000421635420 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635420 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/437 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635420 none C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 40, 40, 50, 50, 50, 50, 8, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/438 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635420 none C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 50, 50, 50, 50, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635420 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 Building ZINC000421635420 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421635420 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 437) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421635420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635420 none C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 40, 40, 50, 50, 50, 50, 8, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 438) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000421635420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421635420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421635420 none C[C@@H]1CC[C@@H](C(=O)OC(C)(C)C)CN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 50, 50, 50, 50, 6, 5, 2, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421635420 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421635420 Building ZINC000421667542 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667542 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/439 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667542 none CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/440 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667542 none CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667542 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 Building ZINC000421667542 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667542 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 439) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667542 none CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 440) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667542 none CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667542 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667542 Building ZINC000421667544 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667544 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/441 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667544 none CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/442 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667544 none CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667544 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 Building ZINC000421667544 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667544 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 441) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667544 none CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 442) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667544 none CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 4, 11, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 3, 6, 6, 13, 13, 13, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667544 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667544 Building ZINC000421667546 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667546 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/443 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667546 none CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 2, 6, 6, 15, 15, 15, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/444 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667546 none CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 3, 6, 6, 14, 14, 14, 6, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667546 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 Building ZINC000421667546 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667546 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 443) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667546 none CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 6, 6, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 2, 6, 6, 15, 15, 15, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 444) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667546 none CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 3, 6, 6, 14, 14, 14, 6, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667546 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667546 Building ZINC000421667548 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667548 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/445 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667548 none CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 4, 10, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 3, 6, 6, 14, 14, 14, 6, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/446 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667548 none CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 6, 6, 3, 6, 15, 6, 6, 6, 12, 12, 12, 19, 19, 19, 19, 19, 12, 12, 2, 6, 6, 15, 15, 15, 6, 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, 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/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667548 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 Building ZINC000421667548 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421667548 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 445) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421667548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667548 none CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 4, 10, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 3, 6, 6, 14, 14, 14, 6, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 446) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1) `ZINC000421667548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421667548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000421667548 none CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 6, 6, 3, 6, 15, 6, 6, 6, 12, 12, 12, 19, 19, 19, 19, 19, 12, 12, 2, 6, 6, 15, 15, 15, 6, 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, 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/74215/xan-8058115.14/working/building/ZINC000421667548 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421667548 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421667548 Building ZINC000421674034 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674034 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/447 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674034 none CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 31, 31, 31, 31, 12, 31, 4, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 31, 31, 31, 42, 42, 42, 42, 42, 31, 31, 4, 4, 4, 4, 4, 31, 31, 31, 31] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/448 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674034 none CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 27, 27, 27, 27, 12, 27, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 42, 42, 42, 42, 42, 27, 27, 5, 5, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674034 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 Building ZINC000421674034 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674034 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 447) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674034 none CC[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 31, 31, 31, 31, 12, 31, 4, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 31, 31, 31, 42, 42, 42, 42, 42, 31, 31, 4, 4, 4, 4, 4, 31, 31, 31, 31] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 448) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674034 none CC[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 27, 27, 27, 27, 12, 27, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 42, 42, 42, 42, 42, 27, 27, 5, 5, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674034 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674034 Building ZINC000421674035 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674035 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/449 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674035 none CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 33, 33, 33, 33, 9, 33, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 44, 44, 44, 44, 44, 33, 33, 5, 5, 5, 5, 5, 33, 33, 33, 33] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/450 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674035 none CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 29, 29, 29, 29, 8, 29, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 29, 29, 29, 42, 42, 42, 42, 42, 29, 29, 4, 5, 5, 5, 5, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674035 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 Building ZINC000421674035 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674035 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 449) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674035 none CC[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 33, 33, 33, 33, 9, 33, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 44, 44, 44, 44, 44, 33, 33, 5, 5, 5, 5, 5, 33, 33, 33, 33] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 450) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674035 none CC[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 29, 29, 29, 29, 8, 29, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 29, 29, 29, 42, 42, 42, 42, 42, 29, 29, 4, 5, 5, 5, 5, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674035 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674035 Building ZINC000421674036 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674036 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/451 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674036 none CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [43, 29, 29, 29, 29, 10, 29, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 43, 43, 43, 43, 43, 29, 29, 4, 5, 5, 5, 5, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/452 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674036 none CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 32, 32, 32, 32, 10, 32, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 44, 44, 44, 44, 44, 32, 32, 5, 5, 5, 5, 5, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674036 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 Building ZINC000421674036 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674036 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 451) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674036 none CC[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [43, 29, 29, 29, 29, 10, 29, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 43, 43, 43, 43, 43, 29, 29, 4, 5, 5, 5, 5, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 452) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674036 none CC[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 32, 32, 32, 32, 10, 32, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 44, 44, 44, 44, 44, 32, 32, 5, 5, 5, 5, 5, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674036 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674036 Building ZINC000421674037 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674037 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/453 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674037 none CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 27, 27, 27, 27, 8, 27, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 27, 27, 27, 42, 42, 42, 42, 42, 27, 27, 5, 5, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/454 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674037 none CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 30, 30, 30, 30, 7, 30, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 42, 42, 42, 42, 42, 30, 30, 4, 4, 4, 4, 4, 30, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674037 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 Building ZINC000421674037 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421674037 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 453) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421674037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674037 none CC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 27, 27, 27, 27, 8, 27, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 27, 27, 27, 42, 42, 42, 42, 42, 27, 27, 5, 5, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 454) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000421674037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421674037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000421674037 none CC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 30, 30, 30, 30, 7, 30, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 42, 42, 42, 42, 42, 30, 30, 4, 4, 4, 4, 4, 30, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421674037 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421674037 Building ZINC000421694015 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000421694015 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/455 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/456 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/457 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/457' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/458 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/458' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421694015 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 Building ZINC000421694015 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000421694015 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 455) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 456) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 457) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 458) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421694015 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 Building ZINC000421694015 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000421694015 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 455) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 456) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 457) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 458) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421694015 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 Building ZINC000421694015 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000421694015 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 455) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 456) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 457) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 12, 12, 12, 12, 12, 29, 30, 30, 30, 12, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 458) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1) `ZINC000421694015.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000421694015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000421694015 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 5, 11, 11, 11, 11, 11, 27, 27, 27, 27, 11, 5, 5, 5, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421694015 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421694015 Building ZINC000421707715 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421707715 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/459 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000421707715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421707715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000421707715 none COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 19, 26, 26, 26, 19, 19, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/460 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000421707715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421707715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000421707715 none COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 19, 26, 26, 26, 19, 19, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421707715 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 Building ZINC000421707715 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421707715 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 459) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000421707715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421707715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000421707715 none COC(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 19, 26, 26, 26, 19, 19, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 460) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000421707715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421707715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000421707715 none COC(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 19, 26, 26, 26, 19, 19, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421707715 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421707715 Building ZINC000421736701 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421736701 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/461 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000421736701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421736701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421736701 none CC(C)n1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 16, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 26, 26, 26, 26, 26, 26, 26, 16, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/462 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000421736701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421736701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421736701 none CC(C)n1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 16, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 26, 26, 26, 26, 26, 26, 26, 16, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421736701 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 Building ZINC000421736701 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000421736701 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 461) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000421736701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000421736701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421736701 none CC(C)n1cc(C(C)(C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 16, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 26, 26, 26, 26, 26, 26, 26, 16, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 462) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1) `ZINC000421736701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000421736701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000421736701 none CC(C)n1cc(C(C)(C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 16, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 26, 26, 26, 26, 26, 26, 26, 16, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000421736701 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000421736701 Building ZINC000195349928 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195349928 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/463 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195349928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349928 none CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 21, 18, 4, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/464 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195349928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349928 none CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 19, 18, 8, 4, 9, 9, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195349928 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 Building ZINC000195349928 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195349928 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 463) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195349928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349928 none CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 21, 18, 4, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 464) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195349928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349928 none CC(C)CCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 19, 18, 8, 4, 9, 9, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195349928 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349928 Building ZINC000195349932 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195349932 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/465 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195349932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349932 none CC(C)CCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 20, 17, 4, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/466 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195349932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349932 none CC(C)CCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 20, 19, 4, 4, 9, 9, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195349932 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 Building ZINC000195349932 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195349932 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 465) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195349932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349932 none CC(C)CCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 20, 17, 4, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 466) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1) `ZINC000195349932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195349932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000195349932 none CC(C)CCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 20, 19, 4, 4, 9, 9, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000195349932 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000195349932 Building ZINC000150810222 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000150810222 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/467 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000150810222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000150810222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000150810222 none CCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 27, 27, 27, 27, 27, 27, 27, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 12, 12, 3, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/468 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000150810222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000150810222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000150810222 none CCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 27, 27, 27, 24, 27, 27, 27, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 12, 12, 3, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000150810222 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 Building ZINC000150810222 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000150810222 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 467) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000150810222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000150810222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000150810222 none CCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 27, 27, 27, 27, 27, 27, 27, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 12, 12, 3, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 468) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000150810222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000150810222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000150810222 none CCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 27, 27, 27, 24, 27, 27, 27, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 12, 12, 3, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000150810222 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000150810222 Building ZINC000491003693 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491003693 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/469 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491003693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003693 none C[C@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 9, 33, 33, 33, 33, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 9, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/470 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491003693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003693 none C[C@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 32, 32, 32, 32, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 10, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000491003693 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 Building ZINC000491003693 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491003693 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 469) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491003693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003693 none C[C@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 9, 33, 33, 33, 33, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 9, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 470) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491003693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003693 none C[C@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 32, 32, 32, 32, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 10, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000491003693 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003693 Building ZINC000491003694 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491003694 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/471 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491003694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003694 none C[C@@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 28, 28, 28, 28, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 10, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/472 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491003694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003694 none C[C@@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 29, 29, 29, 29, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 10, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000491003694 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 Building ZINC000491003694 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000491003694 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 471) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000491003694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003694 none C[C@@H](C1CC1)n1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 28, 28, 28, 28, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 10, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 472) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000491003694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000491003694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000491003694 none C[C@@H](C1CC1)n1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 29, 29, 29, 29, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 10, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000491003694 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000491003694 Building ZINC000125792565 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125792565 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/473 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1) `ZINC000125792565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125792565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000125792565 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 33, 33, 33, 33, 33, 17, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 17, 33, 33, 33, 17, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/474 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1) `ZINC000125792565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125792565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000125792565 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 17, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 17, 32, 32, 32, 17, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125792565 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 Building ZINC000125792565 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000125792565 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 473) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1) `ZINC000125792565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000125792565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000125792565 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 33, 33, 33, 33, 33, 17, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 17, 33, 33, 33, 17, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 474) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1) `ZINC000125792565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000125792565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000125792565 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(c3noc(C)n3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 17, 6, 6, 6, 6, 6, 6, 6, 3, 17, 17, 17, 32, 32, 32, 17, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000125792565 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000125792565 Building ZINC000159215849 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000159215849 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/475 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000159215849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000159215849 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 4, 4, 8, 8, 21, 21, 21, 38, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 21, 21, 21, 38, 38, 46, 46, 92, 46, 46, 4, 4] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/476 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000159215849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000159215849 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 7, 7, 19, 19, 19, 39, 45, 45, 39, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 19, 19, 19, 39, 39, 45, 45, 90, 45, 45, 6, 6] 100 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 314 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000159215849 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 Building ZINC000159215849 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000159215849 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 475) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000159215849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000159215849 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 4, 4, 8, 8, 21, 21, 21, 38, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 21, 21, 21, 38, 38, 46, 46, 92, 46, 46, 4, 4] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 476) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1) `ZINC000159215849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000159215849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000159215849 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc2ccc(O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 7, 7, 19, 19, 19, 39, 45, 45, 39, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 19, 19, 19, 39, 39, 45, 45, 90, 45, 45, 6, 6] 100 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 314 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000159215849 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000159215849 Building ZINC000186958475 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186958475 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/477 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186958475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186958475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000186958475 none CN(CC1(O)CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 5, 18, 26, 26, 26, 26, 26, 26, 26, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 10, 10, 78, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/478 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186958475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186958475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000186958475 none CN(CC1(O)CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 5, 17, 25, 25, 25, 25, 25, 25, 25, 1, 3, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 5, 5, 5, 10, 10, 75, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000186958475 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 Building ZINC000186958475 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186958475 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 477) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186958475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186958475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000186958475 none CN(CC1(O)CCCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 5, 18, 26, 26, 26, 26, 26, 26, 26, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 10, 10, 78, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 478) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(O)CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186958475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186958475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000186958475 none CN(CC1(O)CCCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 5, 17, 25, 25, 25, 25, 25, 25, 25, 1, 3, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 5, 5, 5, 10, 10, 75, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000186958475 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000186958475 Building ZINC000156455179 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156455179 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/479 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(CCO)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156455179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156455179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000156455179 none O=C(NCC1(CCO)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 23, 28, 28, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 28, 28, 28, 28, 84, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/480 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(CCO)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156455179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156455179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000156455179 none O=C(NCC1(CCO)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 23, 27, 27, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 27, 27, 27, 27, 81, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000156455179 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 Building ZINC000156455179 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156455179 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 479) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(CCO)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156455179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156455179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000156455179 none O=C(NCC1(CCO)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 23, 28, 28, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 28, 28, 28, 28, 84, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 480) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(CCO)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156455179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156455179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000156455179 none O=C(NCC1(CCO)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 23, 27, 27, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 27, 27, 27, 27, 81, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000156455179 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156455179 Building ZINC000936643102 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936643102 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/481 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/481' -> `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]2C[C@H]1CN2C(=O)CCC1CCCCC1) `ZINC000936643102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936643102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936643102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 19, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/482 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/482' -> `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]2C[C@H]1CN2C(=O)CCC1CCCCC1) `ZINC000936643102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936643102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936643102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 16, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936643102 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 Building ZINC000936643102 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936643102 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 481) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CCC1CCCCC1) `ZINC000936643102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936643102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936643102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 19, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 482) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CCC1CCCCC1) `ZINC000936643102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936643102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000936643102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C[C@H]1CN2C(=O)CCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 16, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936643102 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936643102 Building ZINC000936642549 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936642549 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/483 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936642549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642549 none CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 18, 50, 6, 18, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/484 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936642549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642549 none CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 19, 50, 5, 19, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936642549 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 Building ZINC000936642549 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936642549 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 483) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936642549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642549 none CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 18, 50, 6, 18, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 484) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936642549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642549 none CC1=C(C)C[C@@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 19, 50, 5, 19, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936642549 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642549 Building ZINC000936642551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936642551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/485 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936642551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642551 none CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 19, 50, 6, 19, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/486 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936642551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642551 none CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 18, 50, 5, 18, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936642551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 Building ZINC000936642551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000936642551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 485) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000936642551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642551 none CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 19, 50, 6, 19, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 486) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC000936642551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000936642551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000936642551 none CC1=C(C)C[C@H](C(=O)N2C[C@@H]3C[C@H]2CN3C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 18, 50, 5, 18, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000936642551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000936642551 Building ZINC000163602003 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163602003 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/487 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1) `ZINC000163602003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163602003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000163602003 none Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 4, 4, 4, 4] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/488 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1) `ZINC000163602003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163602003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000163602003 none Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 4, 4, 4, 4] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000163602003 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 Building ZINC000163602003 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163602003 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 487) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1) `ZINC000163602003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163602003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000163602003 none Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 4, 4, 4, 4] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 488) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1) `ZINC000163602003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163602003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000163602003 none Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 4, 4, 4, 4] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000163602003 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000163602003 Building ZINC000343916865 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343916865 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/489 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343916865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000343916865 none Cc1noc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 9, 3, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/490 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343916865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000343916865 none Cc1noc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 7, 3, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343916865 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 Building ZINC000343916865 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343916865 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 489) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343916865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000343916865 none Cc1noc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 9, 3, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 490) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343916865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000343916865 none Cc1noc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 7, 3, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343916865 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343916865 Building ZINC000245719539 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000245719539 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/491 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000245719539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719539 none O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/492 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000245719539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719539 none O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000245719539 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 Building ZINC000245719539 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000245719539 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 491) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000245719539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719539 none O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 492) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000245719539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719539 none O=C(N[C@@H]1[C@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000245719539 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719539 Building ZINC000245719545 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000245719545 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/493 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000245719545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719545 none O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 12, 12, 16, 16, 12, 16, 16, 16, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/494 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000245719545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719545 none O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 16, 16, 11, 16, 16, 16, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000245719545 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 Building ZINC000245719545 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000245719545 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 493) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000245719545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719545 none O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 12, 12, 16, 16, 12, 16, 16, 16, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 494) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000245719545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000245719545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000245719545 none O=C(N[C@@H]1[C@@H]2CCO[C@H]2C12CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 16, 16, 11, 16, 16, 16, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000245719545 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000245719545 Building ZINC000156530362 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156530362 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/495 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156530362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156530362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000156530362 none O=C(N1CCN(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 11, 18, 18, 18, 18, 30, 30, 30, 30, 18, 18, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 18, 18, 18, 18, 2, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/496 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156530362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156530362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000156530362 none O=C(N1CCN(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 10, 12, 12, 12, 12, 27, 27, 27, 27, 12, 12, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 12, 12, 12, 12, 27, 27, 27, 12, 12, 12, 12, 2, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000156530362 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 Building ZINC000156530362 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156530362 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 495) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156530362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156530362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000156530362 none O=C(N1CCN(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 11, 18, 18, 18, 18, 30, 30, 30, 30, 18, 18, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 18, 18, 18, 18, 30, 30, 30, 18, 18, 18, 18, 2, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 496) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000156530362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156530362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000156530362 none O=C(N1CCN(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 10, 12, 12, 12, 12, 27, 27, 27, 27, 12, 12, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 12, 12, 12, 12, 27, 27, 27, 12, 12, 12, 12, 2, 4, 4, 4, 4, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000156530362 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156530362 Building ZINC000343941164 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941164 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/497 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941164 none CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 7, 20, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/498 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941164 none CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 7, 20, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 16, 16, 16, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343941164 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 Building ZINC000343941164 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941164 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 497) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941164 none CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 7, 20, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 498) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941164 none CC(C)(C)[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 7, 20, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 16, 16, 16, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343941164 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343941164 Building ZINC000124687891 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124687891 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/499 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000124687891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124687891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000124687891 none Cn1nccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 50, 50, 50, 22, 22, 22, 22, 8, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 3, 3, 3, 3, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/500 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000124687891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124687891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000124687891 none Cn1nccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 50, 50, 50, 23, 23, 23, 23, 8, 1, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 3, 3, 3, 3, 23, 23, 23, 23] 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: 93 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124687891 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 Building ZINC000124687891 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000124687891 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 499) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000124687891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000124687891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000124687891 none Cn1nccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 50, 50, 50, 22, 22, 22, 22, 8, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 3, 3, 3, 3, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 500) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000124687891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000124687891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000124687891 none Cn1nccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 50, 50, 50, 50, 23, 23, 23, 23, 8, 1, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 3, 3, 3, 3, 23, 23, 23, 23] 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: 93 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000124687891 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000124687891 Building ZINC000611355209 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611355209 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/501 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000611355209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611355209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000611355209 none CC(C)(C)OC(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 14, 30, 10, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 10, 10, 10, 10, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/502 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000611355209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611355209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000611355209 none CC(C)(C)OC(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 31, 15, 31, 11, 8, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 11, 11, 11, 11, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000611355209 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 Building ZINC000611355209 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611355209 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 501) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000611355209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611355209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000611355209 none CC(C)(C)OC(=O)CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 14, 30, 10, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 10, 10, 10, 10, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 502) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000611355209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611355209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000611355209 none CC(C)(C)OC(=O)CCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 31, 15, 31, 11, 8, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 11, 11, 11, 11, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000611355209 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611355209 Building ZINC000106491322 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106491322 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/503 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106491322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491322 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 24, 24, 24, 24, 41, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 24, 24, 41, 41, 41, 24, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/504 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106491322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491322 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 24, 24, 24, 24, 41, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 24, 24, 41, 41, 41, 24, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106491322 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 Building ZINC000106491322 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106491322 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 503) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106491322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491322 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 24, 24, 24, 24, 41, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 24, 24, 41, 41, 41, 24, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 504) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106491322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491322 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 24, 24, 24, 24, 41, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 24, 24, 41, 41, 41, 24, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106491322 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491322 Building ZINC000106491325 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106491325 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/505 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106491325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491325 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 24, 24, 24, 24, 42, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 24, 24, 42, 42, 42, 24, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/506 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106491325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491325 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 23, 23, 23, 23, 40, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 23, 23, 40, 40, 40, 23, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106491325 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 Building ZINC000106491325 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106491325 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 505) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106491325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491325 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 24, 24, 24, 24, 42, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 24, 24, 42, 42, 42, 24, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 506) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1) `ZINC000106491325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106491325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106491325 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(OC)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 23, 23, 23, 23, 40, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 23, 23, 40, 40, 40, 23, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106491325 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106491325 Building ZINC000106492495 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106492495 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/507 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1) `ZINC000106492495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106492495 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 29, 29, 22, 29, 29, 29, 42, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 29, 29, 29, 29, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/508 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1) `ZINC000106492495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106492495 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 29, 29, 29, 29, 29, 29, 42, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 29, 29, 29, 29, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492495 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 Building ZINC000106492495 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106492495 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 507) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1) `ZINC000106492495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106492495 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 29, 29, 22, 29, 29, 29, 42, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 29, 29, 29, 29, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 508) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1) `ZINC000106492495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106492495 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 29, 29, 29, 29, 29, 29, 42, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 29, 29, 29, 29, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492495 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492495 Building ZINC000106492916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106492916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/509 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/510 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/511 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/511' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/512 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/512' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 Building ZINC000106492916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106492916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 509) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 510) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 511) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 512) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 Building ZINC000106492916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106492916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 509) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 510) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 511) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 512) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 Building ZINC000106492916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106492916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 509) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 510) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 23, 28, 28, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 21, 21, 22, 23, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 511) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 512) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1) `ZINC000106492916.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106492916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106492916 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 18, 24, 29, 29, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 23, 23, 24, 24, 29, 29, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492916 Building ZINC000106492965 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106492965 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/513 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492965 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 31, 31, 31, 31, 31, 40, 40, 40, 31, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 31, 31, 31, 40, 40, 40, 40, 31, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/514 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492965 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 34, 34, 34, 34, 34, 42, 42, 42, 34, 5, 5, 5, 5, 5, 5, 5, 4, 7, 7, 7, 34, 34, 34, 42, 42, 42, 42, 34, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492965 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 Building ZINC000106492965 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106492965 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 513) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492965 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 31, 31, 31, 31, 31, 40, 40, 40, 31, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 31, 31, 31, 40, 40, 40, 40, 31, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 514) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492965 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 34, 34, 34, 34, 34, 42, 42, 42, 34, 5, 5, 5, 5, 5, 5, 5, 4, 7, 7, 7, 34, 34, 34, 42, 42, 42, 42, 34, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492965 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492965 Building ZINC000106492966 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106492966 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/515 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492966 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 34, 34, 34, 34, 34, 41, 41, 41, 34, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 34, 34, 34, 41, 41, 41, 41, 34, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/516 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492966 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 30, 30, 30, 30, 30, 39, 39, 39, 30, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 30, 30, 30, 39, 39, 39, 39, 30, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492966 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 Building ZINC000106492966 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106492966 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 515) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106492966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492966 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 34, 34, 34, 34, 34, 41, 41, 41, 34, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 34, 34, 34, 41, 41, 41, 41, 34, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 516) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1) `ZINC000106492966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106492966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106492966 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(C)=O)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 30, 30, 30, 30, 30, 39, 39, 39, 30, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 30, 30, 30, 39, 39, 39, 39, 30, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106492966 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106492966 Building ZINC000106493098 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106493098 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/517 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1) `ZINC000106493098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106493098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493098 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 11, 15, 42, 50, 50, 15, 15, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/518 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1) `ZINC000106493098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106493098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493098 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 8, 12, 43, 50, 50, 15, 15, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106493098 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 Building ZINC000106493098 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106493098 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 517) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1) `ZINC000106493098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106493098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493098 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 11, 15, 42, 50, 50, 15, 15, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 518) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1) `ZINC000106493098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106493098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493098 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 8, 12, 43, 50, 50, 15, 15, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106493098 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493098 Building ZINC000106493552 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106493552 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/519 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1) `ZINC000106493552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106493552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493552 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 12, 20, 46, 49, 49, 46, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 12, 12, 20, 20, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/520 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1) `ZINC000106493552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106493552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493552 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 13, 21, 46, 49, 49, 46, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 13, 13, 21, 21, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106493552 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 Building ZINC000106493552 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106493552 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 519) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1) `ZINC000106493552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106493552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493552 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 12, 20, 46, 49, 49, 46, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 12, 12, 20, 20, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 520) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1) `ZINC000106493552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106493552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106493552 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCOc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 13, 21, 46, 49, 49, 46, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 13, 13, 21, 21, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106493552 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106493552 Building ZINC000106494230 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494230 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/521 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1) `ZINC000106494230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494230 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 32, 32, 32, 32, 32, 32, 32, 41, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 32, 32, 32, 41, 41, 41, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/522 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1) `ZINC000106494230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494230 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 32, 32, 32, 22, 32, 32, 32, 41, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 32, 32, 32, 41, 41, 41, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494230 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 Building ZINC000106494230 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494230 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 521) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1) `ZINC000106494230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494230 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 32, 32, 32, 32, 32, 32, 32, 41, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 32, 32, 32, 41, 41, 41, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 522) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1) `ZINC000106494230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494230 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 32, 32, 32, 22, 32, 32, 32, 41, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 32, 32, 32, 41, 41, 41, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494230 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494230 Building ZINC000106494797 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494797 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/523 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494797 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 26, 26, 26, 14, 26, 26, 26, 33, 7, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 26, 14, 26, 33, 33, 33, 7, 7] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/524 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494797 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 26, 26, 26, 22, 26, 26, 26, 35, 6, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 26, 16, 26, 35, 35, 35, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494797 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 Building ZINC000106494797 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494797 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 523) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494797 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 26, 26, 26, 14, 26, 26, 26, 33, 7, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 26, 14, 26, 33, 33, 33, 7, 7] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 524) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494797 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 26, 26, 26, 22, 26, 26, 26, 35, 6, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 26, 16, 26, 35, 35, 35, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494797 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494797 Building ZINC000106494800 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494800 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/525 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494800 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 25, 25, 25, 19, 25, 25, 25, 34, 7, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 25, 14, 25, 34, 34, 34, 7, 7] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/526 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494800 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 25, 25, 25, 22, 25, 25, 25, 31, 7, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 25, 16, 25, 31, 31, 31, 7, 7] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494800 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 Building ZINC000106494800 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106494800 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 525) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106494800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494800 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 25, 25, 25, 19, 25, 25, 25, 34, 7, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 25, 14, 25, 34, 34, 34, 7, 7] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 526) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1) `ZINC000106494800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106494800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106494800 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cc(F)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 25, 25, 25, 22, 25, 25, 25, 31, 7, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 25, 16, 25, 31, 31, 31, 7, 7] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106494800 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106494800 Building ZINC000106495546 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495546 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/527 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/528 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/529 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/529' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/530 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/530' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495546 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 Building ZINC000106495546 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495546 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 527) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 528) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 529) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 530) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495546 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 Building ZINC000106495546 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495546 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 527) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 528) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 529) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 530) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495546 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 Building ZINC000106495546 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495546 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 527) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 528) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 31, 20, 20, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 31, 31, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 529) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 530) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1) `ZINC000106495546.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000106495546 none CCCCN(C)CC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 29, 18, 18, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 50, 50, 50, 50, 50, 49, 49, 29, 29, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 50, 49, 11, 44, 13, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495546 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495546 Building ZINC000106495669 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495669 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/531 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/532 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/533 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/533' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/534 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/534' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495669 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 Building ZINC000106495669 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495669 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 531) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 532) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 533) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 534) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495669 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 Building ZINC000106495669 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495669 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 531) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 532) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 533) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 534) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495669 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 Building ZINC000106495669 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495669 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 531) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 532) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 533) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 8, 18, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 50, 50, 32, 50, 50, 21, 21, 21, 21, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 534) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1) `ZINC000106495669.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495669 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 16, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 49, 49, 34, 49, 49, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495669 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495669 Building ZINC000106495736 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495736 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/535 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1) `ZINC000106495736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106495736 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 24, 24, 24, 24, 24, 24, 42, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/536 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1) `ZINC000106495736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106495736 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 25, 25, 18, 25, 25, 25, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495736 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 Building ZINC000106495736 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495736 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 535) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1) `ZINC000106495736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106495736 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 24, 24, 24, 24, 24, 24, 42, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 536) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1) `ZINC000106495736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106495736 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2OC(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 25, 25, 18, 25, 25, 25, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495736 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495736 Building ZINC000106495826 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495826 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/537 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/538 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/539 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/539' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/540 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/540' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495826 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 Building ZINC000106495826 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495826 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 537) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 538) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 539) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 540) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495826 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 Building ZINC000106495826 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495826 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 537) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 538) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 539) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 540) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495826 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 Building ZINC000106495826 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495826 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 537) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 538) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 539) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 540) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495826 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495826 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495826 Building ZINC000106495829 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495829 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/541 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/542 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/543 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/543' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/544 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/544' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495829 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 Building ZINC000106495829 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495829 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 541) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 542) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 543) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 544) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495829 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 Building ZINC000106495829 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495829 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 541) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 542) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 543) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 544) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495829 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 Building ZINC000106495829 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000106495829 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 541) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 542) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 543) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 544) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1) `ZINC000106495829.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000106495829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000106495829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCN(C)c3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495829 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495829 Building ZINC000106495958 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495958 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/545 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106495958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106495958 none COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 24, 47, 47, 22, 17, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 47, 47, 47, 47, 47, 47, 47, 22, 22, 18, 18, 13, 13, 5, 5, 5, 2, 2, 4, 4, 4, 2, 2, 47, 47] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/546 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106495958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106495958 none COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 45, 21, 16, 12, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 45, 45, 45, 45, 45, 45, 45, 21, 21, 17, 17, 12, 12, 4, 4, 4, 2, 2, 4, 4, 4, 2, 2, 45, 45] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495958 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 Building ZINC000106495958 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495958 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 545) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106495958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106495958 none COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 24, 47, 47, 22, 17, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 47, 47, 47, 47, 47, 47, 47, 22, 22, 18, 18, 13, 13, 5, 5, 5, 2, 2, 4, 4, 4, 2, 2, 47, 47] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 546) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106495958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106495958 none COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 45, 21, 16, 12, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 45, 45, 45, 45, 45, 45, 45, 21, 21, 17, 17, 12, 12, 4, 4, 4, 2, 2, 4, 4, 4, 2, 2, 45, 45] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495958 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495958 Building ZINC000106495989 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495989 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/547 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495989 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 2, 7, 7, 1, 1, 1, 1, 4, 4, 4, 25, 38, 40, 40, 38, 38, 38, 38, 38, 38, 38, 7, 7, 7, 7, 7, 7, 7, 4, 23, 23, 40, 40, 40, 40, 40, 40, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/548 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495989 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 26, 38, 39, 39, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 5, 25, 25, 39, 39, 39, 39, 39, 39, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495989 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 Building ZINC000106495989 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495989 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 547) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495989 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 2, 7, 7, 1, 1, 1, 1, 4, 4, 4, 25, 38, 40, 40, 38, 38, 38, 38, 38, 38, 38, 7, 7, 7, 7, 7, 7, 7, 4, 23, 23, 40, 40, 40, 40, 40, 40, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 548) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495989 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 26, 38, 39, 39, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 5, 25, 25, 39, 39, 39, 39, 39, 39, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495989 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495989 Building ZINC000106495992 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495992 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/549 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495992 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/550 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495992 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 40, 41, 41, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 41, 41, 41, 41, 41, 41, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495992 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 Building ZINC000106495992 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495992 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 549) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495992 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 550) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495992 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 40, 41, 41, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 41, 41, 41, 41, 41, 41, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495992 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495992 Building ZINC000106495995 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495995 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/551 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495995 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 40, 42, 42, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 42, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/552 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495995 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 39, 43, 43, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 43, 43, 43, 43, 43, 43, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495995 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 Building ZINC000106495995 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495995 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 551) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495995 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 19, 40, 42, 42, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 42, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 552) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1) `ZINC000106495995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495995 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 18, 39, 43, 43, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 43, 43, 43, 43, 43, 43, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495995 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495995 Building ZINC000106495998 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495998 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/553 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495998 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 21, 38, 39, 39, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 39, 39, 39, 39, 39, 39, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/554 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495998 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495998 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 Building ZINC000106495998 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106495998 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 553) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106495998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495998 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 21, 38, 39, 39, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 39, 39, 39, 39, 39, 39, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 554) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1) `ZINC000106495998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106495998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000106495998 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N(C)C)CCC[C@H](C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6, 6, 5, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106495998 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106495998 Building ZINC000106496173 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496173 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/555 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1) `ZINC000106496173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496173 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 5, 5, 5, 12, 27, 50, 50, 27, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 12, 12, 50, 50, 27, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/556 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1) `ZINC000106496173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496173 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 28, 49, 49, 28, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 14, 14, 49, 49, 28, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496173 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 Building ZINC000106496173 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496173 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 555) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1) `ZINC000106496173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496173 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 5, 5, 5, 12, 27, 50, 50, 27, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 12, 12, 50, 50, 27, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 556) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1) `ZINC000106496173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496173 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 28, 49, 49, 28, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 14, 14, 49, 49, 28, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496173 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496173 Building ZINC000106496177 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496177 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/557 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1) `ZINC000106496177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496177 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 28, 50, 50, 49, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 14, 14, 50, 50, 49, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/558 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1) `ZINC000106496177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496177 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 5, 5, 5, 12, 27, 50, 50, 27, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 12, 12, 50, 50, 27, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496177 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 Building ZINC000106496177 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496177 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 557) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1) `ZINC000106496177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496177 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 28, 50, 50, 49, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 14, 14, 50, 50, 49, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 558) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1) `ZINC000106496177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106496177 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)COc2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 5, 5, 5, 12, 27, 50, 50, 27, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 12, 12, 50, 50, 27, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496177 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496177 Building ZINC000106496253 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496253 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/559 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1) `ZINC000106496253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496253 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 11, 19, 36, 50, 50, 36, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 8, 8, 8, 11, 11, 36, 36, 50, 50, 36, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/560 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1) `ZINC000106496253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496253 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 12, 20, 37, 50, 50, 37, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 9, 9, 9, 12, 12, 37, 37, 50, 50, 37, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496253 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 Building ZINC000106496253 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496253 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 559) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1) `ZINC000106496253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496253 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 11, 19, 36, 50, 50, 36, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 8, 8, 8, 11, 11, 36, 36, 50, 50, 36, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 560) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1) `ZINC000106496253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496253 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 12, 20, 37, 50, 50, 37, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 9, 9, 9, 12, 12, 37, 37, 50, 50, 37, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496253 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496253 Building ZINC000106496255 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496255 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/561 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1) `ZINC000106496255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496255 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 11, 19, 35, 50, 50, 35, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 8, 8, 8, 11, 11, 35, 35, 50, 50, 35, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/562 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1) `ZINC000106496255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496255 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 11, 19, 37, 50, 50, 37, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 8, 8, 8, 11, 11, 37, 37, 50, 50, 37, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496255 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 Building ZINC000106496255 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496255 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 561) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1) `ZINC000106496255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496255 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 11, 19, 35, 50, 50, 35, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 8, 8, 8, 11, 11, 35, 35, 50, 50, 35, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 562) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1) `ZINC000106496255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106496255 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 11, 19, 37, 50, 50, 37, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 8, 8, 8, 11, 11, 37, 37, 50, 50, 37, 50, 50, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496255 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496255 Building ZINC000106496358 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496358 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/563 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1) `ZINC000106496358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496358 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 23, 23, 23, 23, 6, 19, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 13, 13, 23, 23, 23, 10, 10, 24, 24, 24, 24, 24, 24, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/564 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1) `ZINC000106496358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496358 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 6, 14, 21, 21, 21, 21, 6, 23, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 14, 14, 21, 21, 21, 14, 14, 27, 27, 27, 27, 27, 27, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496358 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 Building ZINC000106496358 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496358 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 563) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1) `ZINC000106496358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496358 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 23, 23, 23, 23, 6, 19, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 13, 13, 23, 23, 23, 10, 10, 24, 24, 24, 24, 24, 24, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 564) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1) `ZINC000106496358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496358 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 6, 14, 21, 21, 21, 21, 6, 23, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 14, 14, 21, 21, 21, 14, 14, 27, 27, 27, 27, 27, 27, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496358 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496358 Building ZINC000106496360 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496360 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/565 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1) `ZINC000106496360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496360 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 6, 14, 22, 22, 22, 22, 6, 22, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 14, 14, 22, 22, 22, 14, 14, 26, 26, 26, 26, 26, 26, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/566 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1) `ZINC000106496360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496360 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 15, 25, 25, 25, 25, 6, 19, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 15, 15, 25, 25, 25, 11, 11, 25, 25, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496360 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 Building ZINC000106496360 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496360 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 565) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1) `ZINC000106496360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496360 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 6, 14, 22, 22, 22, 22, 6, 22, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 14, 14, 22, 22, 22, 14, 14, 26, 26, 26, 26, 26, 26, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 566) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1) `ZINC000106496360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496360 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)C[C@H]2CCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 15, 25, 25, 25, 25, 6, 19, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 15, 15, 25, 25, 25, 11, 11, 25, 25, 25, 25, 25, 25, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496360 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496360 Building ZINC000106496410 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496410 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/567 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1) `ZINC000106496410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496410 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 32, 49, 49, 32, 49, 49, 7, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 49, 49, 32, 49, 49, 7, 7, 7, 7, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/568 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1) `ZINC000106496410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496410 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 28, 47, 47, 28, 47, 47, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 47, 47, 28, 47, 47, 7, 7, 7, 7, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496410 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 Building ZINC000106496410 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106496410 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 567) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1) `ZINC000106496410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106496410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496410 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 32, 49, 49, 32, 49, 49, 7, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 49, 49, 32, 49, 49, 7, 7, 7, 7, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 568) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1) `ZINC000106496410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106496410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106496410 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Oc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 28, 47, 47, 28, 47, 47, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 47, 47, 28, 47, 47, 7, 7, 7, 7, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106496410 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106496410 Building ZINC000106497129 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497129 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/569 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1) `ZINC000106497129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497129 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 20, 47, 47, 20, 47, 47, 20, 20, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 20, 47, 47, 35, 47, 47, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/570 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1) `ZINC000106497129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497129 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 20, 47, 47, 20, 47, 47, 20, 20, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 20, 47, 47, 34, 47, 47, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497129 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 Building ZINC000106497129 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497129 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 569) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1) `ZINC000106497129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497129 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 20, 47, 47, 20, 47, 47, 20, 20, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 20, 47, 47, 35, 47, 47, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 570) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1) `ZINC000106497129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497129 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 20, 47, 47, 20, 47, 47, 20, 20, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 20, 47, 47, 34, 47, 47, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497129 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497129 Building ZINC000106497490 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497490 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/571 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1) `ZINC000106497490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497490 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 38, 38, 15, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 38, 38, 24, 38, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/572 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1) `ZINC000106497490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497490 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 39, 39, 25, 39, 39, 39, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 39, 39, 25, 39, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497490 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 Building ZINC000106497490 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497490 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 571) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1) `ZINC000106497490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497490 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 38, 38, 15, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 38, 38, 24, 38, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 572) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1) `ZINC000106497490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000106497490 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 39, 39, 25, 39, 39, 39, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 39, 39, 25, 39, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497490 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497490 Building ZINC000106497620 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497620 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/573 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106497620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106497620 none COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 21, 50, 50, 19, 8, 19, 17, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/574 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106497620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106497620 none COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 20, 50, 50, 20, 8, 20, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497620 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 Building ZINC000106497620 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497620 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 573) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106497620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106497620 none COc1ccc(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 21, 50, 50, 19, 8, 19, 17, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 574) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000106497620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106497620 none COc1ccc(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 20, 50, 50, 20, 8, 20, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497620 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497620 Building ZINC000106497637 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497637 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/575 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)CC2) `ZINC000106497637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106497637 none CCOc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 4, 3, 3, 9, 9, 48, 48, 48, 48, 48, 9, 9, 9, 9, 9, 3, 3, 4, 4, 4, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/576 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)CC2) `ZINC000106497637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106497637 none CCOc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 4, 3, 3, 9, 9, 48, 48, 48, 48, 48, 9, 9, 9, 9, 9, 3, 3, 4, 4, 4, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497637 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 Building ZINC000106497637 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106497637 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 575) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)CC2) `ZINC000106497637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106497637 none CCOc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 4, 3, 3, 9, 9, 48, 48, 48, 48, 48, 9, 9, 9, 9, 9, 3, 3, 4, 4, 4, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 576) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)CC2) `ZINC000106497637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106497637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106497637 none CCOc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 4, 3, 3, 9, 9, 48, 48, 48, 48, 48, 9, 9, 9, 9, 9, 3, 3, 4, 4, 4, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106497637 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106497637 Building ZINC000106498131 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498131 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/577 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1) `ZINC000106498131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106498131 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 7, 8, 12, 20, 37, 50, 50, 44, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 8, 8, 8, 8, 12, 12, 37, 37, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/578 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1) `ZINC000106498131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106498131 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 7, 8, 12, 19, 38, 50, 50, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 8, 8, 8, 8, 12, 12, 38, 38, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498131 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 Building ZINC000106498131 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498131 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 577) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1) `ZINC000106498131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106498131 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 7, 8, 12, 20, 37, 50, 50, 44, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 8, 8, 8, 8, 12, 12, 37, 37, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 578) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1) `ZINC000106498131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000106498131 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCCOCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 7, 8, 12, 19, 38, 50, 50, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 8, 8, 8, 8, 12, 12, 38, 38, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498131 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498131 Building ZINC000106498425 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498425 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/579 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1) `ZINC000106498425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000106498425 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 27, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/580 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1) `ZINC000106498425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000106498425 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 27, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498425 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 Building ZINC000106498425 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498425 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 579) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1) `ZINC000106498425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000106498425 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 27, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 580) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1) `ZINC000106498425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000106498425 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(OC3CCCC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 27, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498425 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498425 Building ZINC000106498560 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498560 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/581 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1) `ZINC000106498560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106498560 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 12, 18, 44, 49, 49, 45, 45, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 17, 17, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/582 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1) `ZINC000106498560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106498560 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 12, 18, 44, 49, 49, 44, 44, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 17, 17, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498560 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 Building ZINC000106498560 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498560 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 581) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1) `ZINC000106498560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106498560 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 12, 18, 44, 49, 49, 45, 45, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 17, 17, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 582) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1) `ZINC000106498560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106498560 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 12, 18, 44, 49, 49, 44, 44, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 17, 17, 49, 49, 49, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498560 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498560 Building ZINC000106498693 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498693 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/583 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1) `ZINC000106498693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000106498693 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 30, 50, 50, 30, 50, 50, 30, 30, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 30, 50, 50, 30, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/584 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1) `ZINC000106498693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000106498693 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 30, 50, 50, 30, 50, 50, 30, 30, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 30, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498693 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 Building ZINC000106498693 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106498693 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 583) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1) `ZINC000106498693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106498693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000106498693 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 30, 50, 50, 30, 50, 50, 30, 30, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 30, 50, 50, 30, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 584) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1) `ZINC000106498693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106498693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000106498693 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(c3ccccc3)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 30, 50, 50, 30, 50, 50, 30, 30, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 30, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106498693 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106498693 Building ZINC000106499245 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499245 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/585 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000106499245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000106499245 none CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 42, 26, 26, 26, 26, 26, 26, 17, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 49, 49, 49, 49, 49, 26, 26, 26, 26, 17, 17, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/586 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000106499245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000106499245 none CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 27, 27, 27, 27, 27, 27, 18, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 27, 27, 27, 27, 18, 18, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499245 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 Building ZINC000106499245 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499245 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 585) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000106499245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000106499245 none CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 42, 26, 26, 26, 26, 26, 26, 17, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 49, 49, 49, 49, 49, 26, 26, 26, 26, 17, 17, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 586) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000106499245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000106499245 none CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 27, 27, 27, 27, 27, 27, 18, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 50, 50, 50, 50, 50, 27, 27, 27, 27, 18, 18, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499245 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499245 Building ZINC000106499521 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499521 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/587 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1) `ZINC000106499521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499521 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 27, 27, 14, 26, 50, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 27, 27, 50, 50, 50, 27, 27, 27, 27, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/588 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1) `ZINC000106499521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499521 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 27, 27, 15, 11, 41, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 27, 27, 46, 43, 46, 27, 27, 27, 27, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499521 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 Building ZINC000106499521 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499521 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 587) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1) `ZINC000106499521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499521 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 27, 27, 14, 26, 50, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 27, 27, 50, 50, 50, 27, 27, 27, 27, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 588) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1) `ZINC000106499521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499521 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(OC)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 11, 27, 27, 15, 11, 41, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 27, 27, 46, 43, 46, 27, 27, 27, 27, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499521 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499521 Building ZINC000106499538 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499538 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/589 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1) `ZINC000106499538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499538 none COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 5, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/590 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1) `ZINC000106499538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499538 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 32, 32, 17, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 5, 12, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499538 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 Building ZINC000106499538 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499538 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 589) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1) `ZINC000106499538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499538 none COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 5, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 590) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1) `ZINC000106499538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499538 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 32, 32, 17, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 5, 12, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 32, 32, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499538 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499538 Building ZINC000106499992 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499992 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/591 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1) `ZINC000106499992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499992 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 33, 49, 49, 39, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 9, 9, 11, 11, 49, 49, 42, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/592 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1) `ZINC000106499992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499992 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 32, 49, 49, 40, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 9, 9, 12, 12, 49, 49, 41, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499992 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 Building ZINC000106499992 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106499992 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 591) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1) `ZINC000106499992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106499992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499992 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 33, 49, 49, 39, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 9, 9, 11, 11, 49, 49, 42, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 592) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1) `ZINC000106499992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106499992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000106499992 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCOc2ccccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 32, 49, 49, 40, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 9, 9, 12, 12, 49, 49, 41, 49, 49, 49, 49, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106499992 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106499992 Building ZINC000106500220 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106500220 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/593 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1F) `ZINC000106500220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106500220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000106500220 none CCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 27, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/594 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1F) `ZINC000106500220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106500220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000106500220 none CCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 26, 26, 26, 26, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106500220 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 Building ZINC000106500220 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106500220 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 593) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1F) `ZINC000106500220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106500220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000106500220 none CCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 27, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 594) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1F) `ZINC000106500220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106500220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000106500220 none CCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 26, 26, 26, 26, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000106500220 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000106500220 Building ZINC000611448263 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611448263 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/595 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C) `ZINC000611448263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611448263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000611448263 none COC(=O)c1csc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 22, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 7, 7, 7, 22, 22, 22, 7, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/596 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C) `ZINC000611448263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611448263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000611448263 none COC(=O)c1csc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 8, 8, 24, 24, 24, 8, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000611448263 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 Building ZINC000611448263 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611448263 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 595) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C) `ZINC000611448263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611448263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000611448263 none COC(=O)c1csc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 22, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 7, 7, 7, 22, 22, 22, 7, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 596) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1csc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C) `ZINC000611448263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611448263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000611448263 none COC(=O)c1csc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 8, 8, 24, 24, 24, 8, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000611448263 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611448263 Building ZINC000156668028 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156668028 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/597 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccncc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000156668028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156668028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000156668028 none Cc1cnn(c2ccncc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 13, 13, 13, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/598 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccncc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000156668028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156668028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000156668028 none Cc1cnn(c2ccncc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 14, 14, 14, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000156668028 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 Building ZINC000156668028 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156668028 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 597) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccncc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000156668028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156668028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000156668028 none Cc1cnn(c2ccncc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 13, 13, 13, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 598) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccncc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000156668028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156668028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000156668028 none Cc1cnn(c2ccncc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 14, 14, 14, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000156668028 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000156668028 Building ZINC000856307344 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000856307344 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/599 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1) `ZINC000856307344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000856307344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000856307344 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 17, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 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]) total number of confs: 28 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/600 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1) `ZINC000856307344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000856307344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000856307344 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 17, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 2, 1, 1, 1, 6, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 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: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000856307344 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 Building ZINC000856307344 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000856307344 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 599) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1) `ZINC000856307344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000856307344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000856307344 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 17, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 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]) total number of confs: 28 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 600) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1) `ZINC000856307344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000856307344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000856307344 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCOc2cc(Br)ccc2C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 17, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 2, 1, 1, 1, 6, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 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: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000856307344 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000856307344 Building ZINC000344175621 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344175621 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/601 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344175621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175621 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 21, 21, 21, 12, 21, 21, 21, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/602 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344175621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175621 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 6, 11, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 21, 21, 21, 12, 21, 21, 21, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000344175621 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 Building ZINC000344175621 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344175621 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 601) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344175621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175621 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 10, 21, 21, 21, 12, 21, 21, 21, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 602) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344175621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175621 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 6, 11, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 21, 21, 21, 12, 21, 21, 21, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000344175621 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175621 Building ZINC000344175624 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344175624 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/603 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344175624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175624 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 6, 11, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 11, 21, 21, 21, 17, 21, 21, 21, 11, 11, 11, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/604 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344175624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175624 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 10, 21, 21, 21, 15, 21, 21, 21, 10, 10, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000344175624 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 Building ZINC000344175624 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344175624 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 603) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344175624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175624 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 6, 11, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 11, 21, 21, 21, 17, 21, 21, 21, 11, 11, 11, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 604) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F) `ZINC000344175624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344175624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000344175624 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(F)cncc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 1, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 10, 21, 21, 21, 15, 21, 21, 21, 10, 10, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000344175624 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000344175624 Building ZINC000611656363 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611656363 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/605 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC000611656363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611656363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000611656363 none CCOC(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 15, 50, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 15, 15, 11, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/606 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC000611656363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611656363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000611656363 none CCOC(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 16, 49, 10, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 16, 16, 10, 10, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000611656363 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 Building ZINC000611656363 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611656363 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 605) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC000611656363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611656363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000611656363 none CCOC(=O)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 15, 50, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 15, 15, 11, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 606) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC000611656363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611656363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000611656363 none CCOC(=O)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 16, 49, 10, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 16, 16, 10, 10, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000611656363 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000611656363 Building ZINC000126030429 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000126030429 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/607 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1) `ZINC000126030429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000126030429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000126030429 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 5, 5, 15, 15, 10, 10, 46, 46, 46, 46, 46, 46, 15, 15, 8, 8, 8, 8, 8, 8, 8, 5, 15, 15, 46, 46, 46, 15, 15, 8, 8] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/608 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1) `ZINC000126030429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000126030429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000126030429 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 1, 5, 5, 5, 16, 16, 8, 12, 45, 45, 45, 45, 45, 45, 16, 16, 8, 8, 8, 8, 8, 8, 8, 5, 16, 16, 45, 45, 45, 16, 16, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000126030429 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 Building ZINC000126030429 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000126030429 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 607) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1) `ZINC000126030429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000126030429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000126030429 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 5, 5, 15, 15, 10, 10, 46, 46, 46, 46, 46, 46, 15, 15, 8, 8, 8, 8, 8, 8, 8, 5, 15, 15, 46, 46, 46, 15, 15, 8, 8] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 608) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1) `ZINC000126030429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000126030429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000126030429 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc(C)n[nH]3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 8, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 1, 5, 5, 5, 16, 16, 8, 12, 45, 45, 45, 45, 45, 45, 16, 16, 8, 8, 8, 8, 8, 8, 8, 5, 16, 16, 45, 45, 45, 16, 16, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000126030429 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126030429 Building ZINC000030217231 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030217231 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/609 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)cc2)cc1) `ZINC000030217231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030217231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000030217231 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 1, 2, 2, 2, 8, 18, 18, 10, 18, 26, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 18, 18, 26, 26, 50, 50, 50, 18, 18, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/610 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)cc2)cc1) `ZINC000030217231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030217231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000030217231 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 14, 18, 27, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 18, 18, 27, 27, 50, 50, 50, 18, 18, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000030217231 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 Building ZINC000030217231 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030217231 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 609) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)cc2)cc1) `ZINC000030217231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030217231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000030217231 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 1, 2, 2, 2, 8, 18, 18, 10, 18, 26, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 18, 18, 26, 26, 50, 50, 50, 18, 18, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 610) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)cc2)cc1) `ZINC000030217231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030217231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000030217231 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cn3ccnc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 14, 18, 27, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 18, 18, 27, 27, 50, 50, 50, 18, 18, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000030217231 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000030217231 Building ZINC000173725916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173725916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/611 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173725916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725916 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 2, 7, 7, 1, 1, 1, 2, 17, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 39, 39, 30, 39, 39, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 39, 39, 39, 39, 39, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/612 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173725916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725916 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 2, 15, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 41, 41, 33, 41, 41, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 41, 41, 41, 41, 41, 8, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173725916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 Building ZINC000173725916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173725916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 611) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173725916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725916 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 2, 7, 7, 1, 1, 1, 2, 17, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 39, 39, 30, 39, 39, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 39, 39, 39, 39, 39, 7, 7] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 612) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173725916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725916 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 2, 15, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 41, 41, 33, 41, 41, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 41, 41, 41, 41, 41, 8, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173725916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725916 Building ZINC000173725983 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173725983 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/613 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173725983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725983 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 17, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 40, 40, 29, 40, 40, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 40, 40, 27, 40, 40, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/614 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173725983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725983 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 16, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 43, 43, 28, 43, 43, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 43, 43, 31, 43, 43, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173725983 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 Building ZINC000173725983 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173725983 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 613) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173725983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725983 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 2, 17, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 40, 40, 29, 40, 40, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 40, 40, 27, 40, 40, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 614) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1) `ZINC000173725983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173725983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725983 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OC[C@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 16, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 43, 43, 28, 43, 43, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 43, 43, 31, 43, 43, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173725983 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725983 Building ZINC000173725994 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173725994 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/615 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1) `ZINC000173725994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173725994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725994 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 2, 15, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 43, 43, 27, 43, 43, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 43, 43, 27, 43, 43, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 139 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/616 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1) `ZINC000173725994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173725994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725994 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 2, 18, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 40, 40, 31, 40, 40, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 40, 40, 31, 40, 40, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173725994 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 Building ZINC000173725994 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173725994 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 615) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1) `ZINC000173725994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173725994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725994 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 2, 15, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 43, 43, 27, 43, 43, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 43, 43, 27, 43, 43, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 139 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 616) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1) `ZINC000173725994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173725994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173725994 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OC[C@@H]2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 2, 18, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 40, 40, 31, 40, 40, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 40, 40, 31, 40, 40, 6, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173725994 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173725994 Building ZINC000360429916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360429916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/617 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)O) `ZINC000360429916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360429916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000360429916 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 26, 6, 13, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 13, 32, 32, 32, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 96] 150 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]) total number of confs: 317 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/618 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)O) `ZINC000360429916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360429916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000360429916 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 24, 6, 15, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 15, 30, 30, 30, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 90] 150 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]) total number of confs: 287 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000360429916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 Building ZINC000360429916 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360429916 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 617) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)O) `ZINC000360429916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360429916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000360429916 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 26, 6, 13, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 13, 32, 32, 32, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 96] 150 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]) total number of confs: 317 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 618) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)O) `ZINC000360429916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360429916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000360429916 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C)(C)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 24, 6, 15, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 15, 30, 30, 30, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 90] 150 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]) total number of confs: 287 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000360429916 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000360429916 Building ZINC000907491195 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907491195 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/619 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1) `ZINC000907491195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907491195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907491195 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 5, 5, 9, 9, 18, 18, 9] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/620 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1) `ZINC000907491195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907491195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907491195 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 5, 5, 9, 9, 18, 18, 9] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000907491195 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 Building ZINC000907491195 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907491195 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 619) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1) `ZINC000907491195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907491195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907491195 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 5, 5, 9, 9, 18, 18, 9] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 620) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1) `ZINC000907491195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907491195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907491195 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCc1ccc(OCC(F)(F)F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 5, 5, 9, 9, 18, 18, 9] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000907491195 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000907491195 Building ZINC000112915786 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112915786 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/621 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000112915786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112915786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000112915786 none CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 14, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/622 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000112915786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112915786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000112915786 none CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 21, 16, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112915786 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 Building ZINC000112915786 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112915786 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 621) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000112915786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112915786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000112915786 none CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 14, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 622) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000112915786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112915786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000112915786 none CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 21, 16, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000112915786 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000112915786 Building ZINC000238820353 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238820353 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/623 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238820353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820353 none Cc1ccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6, 39] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/624 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238820353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820353 none Cc1ccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 7, 7, 7, 7, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 3, 3, 3, 3, 3, 7, 7, 39] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238820353 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 Building ZINC000238820353 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238820353 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 623) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238820353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820353 none Cc1ccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6, 39] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 624) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238820353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820353 none Cc1ccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 7, 7, 7, 7, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 3, 3, 3, 3, 3, 7, 7, 39] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238820353 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820353 Building ZINC000238820354 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238820354 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/625 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238820354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820354 none Cc1ccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 7, 7, 7, 7, 7, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 3, 3, 3, 3, 3, 7, 7, 39] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/626 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238820354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820354 none Cc1ccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 5, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 3, 3, 3, 3, 3, 5, 5, 40] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238820354 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 Building ZINC000238820354 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238820354 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 625) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238820354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820354 none Cc1ccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 7, 7, 7, 7, 7, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 3, 3, 3, 3, 3, 7, 7, 39] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 626) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1) `ZINC000238820354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238820354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000238820354 none Cc1ccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 5, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 3, 3, 3, 3, 3, 5, 5, 40] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238820354 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238820354 Building ZINC000238889794 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238889794 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/627 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1) `ZINC000238889794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238889794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238889794 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 21, 33, 33, 33, 33, 33, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 21, 21, 33, 33, 41, 41, 41, 41, 41] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/628 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1) `ZINC000238889794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238889794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238889794 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 20, 37, 37, 37, 37, 37, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 20, 20, 37, 37, 44, 44, 44, 44, 44] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238889794 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 Building ZINC000238889794 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238889794 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 627) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1) `ZINC000238889794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238889794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238889794 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 21, 33, 33, 33, 33, 33, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 21, 21, 33, 33, 41, 41, 41, 41, 41] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 628) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1) `ZINC000238889794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238889794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238889794 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 20, 37, 37, 37, 37, 37, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 20, 20, 37, 37, 44, 44, 44, 44, 44] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238889794 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238889794 Building ZINC000238947845 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238947845 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/629 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1) `ZINC000238947845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238947845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947845 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 27, 44, 44, 44, 44, 44, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 44, 44, 44, 44, 10, 10] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/630 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1) `ZINC000238947845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238947845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947845 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 31, 45, 45, 45, 45, 45, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 45, 45, 45, 45, 9, 9] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238947845 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 Building ZINC000238947845 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238947845 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 629) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1) `ZINC000238947845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238947845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947845 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 27, 44, 44, 44, 44, 44, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 44, 44, 44, 44, 10, 10] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 630) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1) `ZINC000238947845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238947845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947845 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 31, 45, 45, 45, 45, 45, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 45, 45, 45, 45, 9, 9] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238947845 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947845 Building ZINC000238947846 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238947846 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/631 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1) `ZINC000238947846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238947846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947846 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 29, 43, 43, 43, 43, 43, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 43, 43, 43, 43, 9, 9] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/632 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1) `ZINC000238947846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238947846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947846 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 27, 44, 44, 44, 44, 44, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 44, 44, 44, 44, 9, 9] 50 rigid atoms, others: [10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238947846 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 Building ZINC000238947846 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238947846 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 631) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1) `ZINC000238947846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238947846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947846 none Cc1[nH]c2ccccc2c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 29, 43, 43, 43, 43, 43, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 43, 43, 43, 43, 9, 9] 50 rigid atoms, others: [10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 632) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1) `ZINC000238947846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238947846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000238947846 none Cc1[nH]c2ccccc2c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Oc2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 27, 44, 44, 44, 44, 44, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 44, 44, 44, 44, 9, 9] 50 rigid atoms, others: [10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238947846 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238947846 Building ZINC000238962194 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238962194 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/633 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238962194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962194 none Cc1cccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/634 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238962194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962194 none Cc1cccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 20, 6, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238962194 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 Building ZINC000238962194 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238962194 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 633) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238962194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962194 none Cc1cccc(O[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 634) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238962194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962194 none Cc1cccc(O[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 20, 6, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 41, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238962194 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962194 Building ZINC000238962196 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238962196 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/635 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238962196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962196 none Cc1cccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/636 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238962196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962196 none Cc1cccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 3, 3, 3, 3, 3, 5, 5] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238962196 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 Building ZINC000238962196 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000238962196 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 635) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000238962196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962196 none Cc1cccc(O[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 636) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1) `ZINC000238962196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000238962196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000238962196 none Cc1cccc(O[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccccc43)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 3, 3, 3, 3, 3, 5, 5] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000238962196 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000238962196 Building ZINC000152168892 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152168892 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/637 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152168892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168892 none Cc1noc(C)c1[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 20, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 20, 20, 20, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/638 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152168892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168892 none Cc1noc(C)c1[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 16, 11, 16, 16, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 16, 16, 16, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152168892 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 Building ZINC000152168892 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152168892 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 637) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152168892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168892 none Cc1noc(C)c1[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 20, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 20, 20, 20, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 638) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152168892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152168892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000152168892 none Cc1noc(C)c1[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 16, 11, 16, 16, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 16, 16, 16, 11, 11, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152168892 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152168892 Building ZINC000126171339 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000126171339 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/639 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1) `ZINC000126171339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000126171339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000126171339 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 16, 16, 16, 16, 50, 50, 16, 50, 50, 16, 16, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 16, 16, 50, 50, 20, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/640 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1) `ZINC000126171339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000126171339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000126171339 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 7, 7, 14, 14, 14, 14, 50, 50, 18, 50, 50, 14, 14, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 14, 14, 50, 50, 18, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000126171339 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 Building ZINC000126171339 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000126171339 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 639) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1) `ZINC000126171339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000126171339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000126171339 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 16, 16, 16, 16, 50, 50, 16, 50, 50, 16, 16, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 16, 16, 50, 50, 20, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 640) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1) `ZINC000126171339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000126171339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000126171339 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ccc(c3ccccc3)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 7, 7, 14, 14, 14, 14, 50, 50, 18, 50, 50, 14, 14, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 14, 14, 50, 50, 18, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000126171339 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126171339 Building ZINC000908182386 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908182386 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/641 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O) `ZINC000908182386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908182386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908182386 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 11, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 21, 21, 21, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 21, 21, 21, 14] 100 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/642 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O) `ZINC000908182386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908182386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908182386 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 11, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 21, 21, 21, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 21, 21, 21, 14] 100 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908182386 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 Building ZINC000908182386 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908182386 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 641) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O) `ZINC000908182386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908182386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908182386 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 11, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 21, 21, 21, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 21, 21, 21, 14] 100 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 642) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O) `ZINC000908182386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908182386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908182386 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(C(=O)OC)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 11, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 21, 21, 21, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 21, 21, 21, 14] 100 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908182386 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908182386 Building ZINC000748575727 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748575727 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/643 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748575727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575727 none Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 16, 3, 16, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/644 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748575727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575727 none Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 3, 16, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000748575727 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 Building ZINC000748575727 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748575727 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 643) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748575727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575727 none Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 16, 3, 16, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 644) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748575727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575727 none Cc1ccc2c(c1)O[C@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 3, 16, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000748575727 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575727 Building ZINC000748575729 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748575729 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/645 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748575729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575729 none Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 2, 14, 1, 1, 1, 10, 10, 10, 10, 17, 17, 17, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/646 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748575729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575729 none Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000748575729 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 Building ZINC000748575729 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748575729 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 645) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748575729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575729 none Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 2, 14, 1, 1, 1, 10, 10, 10, 10, 17, 17, 17, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 646) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000748575729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748575729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000748575729 none Cc1ccc2c(c1)O[C@@H](C)CN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000748575729 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748575729 Building ZINC000908194424 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908194424 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/647 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000908194424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908194424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908194424 none CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 10, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/648 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000908194424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908194424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908194424 none CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 15, 15, 7, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908194424 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 Building ZINC000908194424 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908194424 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 647) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000908194424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908194424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908194424 none CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 10, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 648) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000908194424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908194424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908194424 none CCCNC(=O)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 15, 15, 7, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908194424 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908194424 Building ZINC000246412246 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000246412246 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/649 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246412246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412246 none CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 12, 12, 12, 12, 12, 4, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/650 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246412246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412246 none CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 27, 12, 12, 12, 12, 12, 4, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000246412246 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 Building ZINC000246412246 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000246412246 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 649) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246412246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412246 none CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 26, 12, 12, 12, 12, 12, 4, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 650) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246412246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412246 none CC[S@](=O)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 27, 12, 12, 12, 12, 12, 4, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000246412246 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412246 Building ZINC000246412263 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000246412263 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/651 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246412263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412263 none CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 18, 28, 18, 18, 18, 18, 18, 5, 18, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 29, 29, 29, 29, 29, 18, 18, 18, 18, 18, 18, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/652 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246412263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412263 none CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 18, 25, 18, 18, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000246412263 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 Building ZINC000246412263 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000246412263 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 651) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000246412263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412263 none CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 18, 28, 18, 18, 18, 18, 18, 5, 18, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 29, 29, 29, 29, 29, 18, 18, 18, 18, 18, 18, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 652) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000246412263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000246412263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000246412263 none CC[S@](=O)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 18, 25, 18, 18, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000246412263 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000246412263 Building ZINC000804152426 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804152426 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/653 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804152426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152426 none CCc1ccc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 32, 32, 16, 11, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 31, 32, 32, 32, 32, 32, 32, 48, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/654 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804152426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152426 none CCc1ccc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 42, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804152426 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 Building ZINC000804152426 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804152426 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 653) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804152426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152426 none CCc1ccc([C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 32, 32, 16, 11, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 31, 32, 32, 32, 32, 32, 32, 48, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 654) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804152426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152426 none CCc1ccc([C@@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 42, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804152426 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152426 Building ZINC000804152427 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804152427 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/655 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804152427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152427 none CCc1ccc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 27, 28, 28, 15, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 45, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/656 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804152427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152427 none CCc1ccc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 31, 31, 31, 31, 16, 11, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 30, 31, 31, 31, 31, 31, 31, 48, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804152427 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 Building ZINC000804152427 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804152427 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 655) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804152427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152427 none CCc1ccc([C@H](O)CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 27, 28, 28, 15, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 45, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 656) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804152427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804152427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804152427 none CCc1ccc([C@H](O)CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 31, 31, 31, 31, 16, 11, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 30, 31, 31, 31, 31, 31, 31, 48, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804152427 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804152427 Building ZINC000748730574 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748730574 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/657 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1) `ZINC000748730574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748730574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748730574 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 14, 14, 29, 29, 29, 29, 29, 29, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/658 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1) `ZINC000748730574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748730574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748730574 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 14, 14, 29, 29, 29, 29, 29, 29, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000748730574 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 Building ZINC000748730574 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748730574 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 657) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1) `ZINC000748730574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748730574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748730574 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 14, 14, 29, 29, 29, 29, 29, 29, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 658) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1) `ZINC000748730574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748730574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748730574 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccnc3ccccc23)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 14, 14, 29, 29, 29, 29, 29, 29, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000748730574 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000748730574 Building ZINC000158456577 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158456577 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/659 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000158456577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158456577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000158456577 none Cn1nc(C2CCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 9, 37, 37, 37, 8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 8, 5, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/660 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000158456577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158456577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000158456577 none Cn1nc(C2CCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 9, 36, 36, 36, 8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 8, 5, 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, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158456577 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 Building ZINC000158456577 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158456577 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 659) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000158456577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158456577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000158456577 none Cn1nc(C2CCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 9, 37, 37, 37, 8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 8, 5, 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, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 660) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000158456577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158456577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000158456577 none Cn1nc(C2CCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 9, 36, 36, 36, 8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 8, 5, 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, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158456577 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158456577 Building ZINC000173947480 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173947480 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/661 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173947480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947480 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 46, 21, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 21, 21, 21, 46, 46, 46, 21, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/662 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173947480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947480 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 24, 24, 24, 24, 24, 47, 47, 47, 47, 24, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 24, 24, 24, 47, 47, 47, 24, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173947480 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 Building ZINC000173947480 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173947480 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 661) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173947480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947480 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 46, 21, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 21, 21, 21, 46, 46, 46, 21, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 662) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173947480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947480 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 24, 24, 24, 24, 24, 47, 47, 47, 47, 24, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 24, 24, 24, 47, 47, 47, 24, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173947480 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947480 Building ZINC000173947494 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173947494 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/663 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173947494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947494 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 25, 25, 25, 25, 25, 48, 48, 48, 48, 25, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 25, 25, 25, 48, 48, 48, 25, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/664 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173947494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947494 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 46, 21, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 21, 21, 21, 46, 46, 46, 21, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173947494 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 Building ZINC000173947494 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173947494 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 663) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173947494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947494 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 25, 25, 25, 25, 25, 48, 48, 48, 48, 25, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 25, 25, 25, 48, 48, 48, 25, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 664) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1) `ZINC000173947494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173947494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000173947494 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3ccnc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 46, 21, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 21, 21, 21, 46, 46, 46, 21, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173947494 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173947494 Building ZINC000173956551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173956551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/665 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173956551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956551 none CC(C)c1csc([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 38, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 25, 38, 38, 38, 38, 38, 38, 38, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/666 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173956551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956551 none CC(C)c1csc([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 25, 25, 25, 5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 5, 25, 34, 34, 34, 34, 34, 34, 34, 25, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173956551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 Building ZINC000173956551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173956551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 665) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173956551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956551 none CC(C)c1csc([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 38, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 25, 38, 38, 38, 38, 38, 38, 38, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 666) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173956551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956551 none CC(C)c1csc([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 25, 25, 25, 5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 5, 25, 34, 34, 34, 34, 34, 34, 34, 25, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173956551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956551 Building ZINC000173956565 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173956565 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/667 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173956565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956565 none CC(C)c1csc([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 25, 25, 25, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 25, 34, 34, 34, 34, 34, 34, 34, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/668 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173956565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956565 none CC(C)c1csc([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 25, 37, 37, 37, 37, 37, 37, 37, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173956565 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 Building ZINC000173956565 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173956565 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 667) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173956565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956565 none CC(C)c1csc([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 25, 25, 25, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 25, 34, 34, 34, 34, 34, 34, 34, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 668) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1csc([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1) `ZINC000173956565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173956565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000173956565 none CC(C)c1csc([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.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', '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, 1, 1, 14, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 25, 37, 37, 37, 37, 37, 37, 37, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000173956565 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000173956565 Building ZINC000052737429 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000052737429 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/669 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000052737429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737429 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 10, 10, 10, 43, 50, 50, 50, 43, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/670 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000052737429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737429 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 42, 50, 50, 50, 42, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000052737429 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 Building ZINC000052737429 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000052737429 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 669) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000052737429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737429 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 10, 10, 10, 43, 50, 50, 50, 43, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 670) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000052737429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737429 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 42, 50, 50, 50, 42, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000052737429 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737429 Building ZINC000052737430 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000052737430 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/671 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000052737430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737430 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 42, 50, 50, 50, 42, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/672 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000052737430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737430 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 10, 10, 10, 43, 50, 50, 50, 43, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000052737430 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 Building ZINC000052737430 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000052737430 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 671) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000052737430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737430 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 42, 50, 50, 50, 42, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 672) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1) `ZINC000052737430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000052737430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000052737430 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 10, 10, 10, 43, 50, 50, 50, 43, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 6, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000052737430 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000052737430 Building ZINC000174088898 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174088898 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/673 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174088898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088898 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 20, 38, 50, 50, 38, 38, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/674 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174088898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088898 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 40, 49, 49, 40, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 20, 20, 20, 49, 49, 49, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174088898 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 Building ZINC000174088898 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174088898 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 673) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174088898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088898 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 20, 38, 50, 50, 38, 38, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 674) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174088898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088898 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 40, 49, 49, 40, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 20, 20, 20, 49, 49, 49, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174088898 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088898 Building ZINC000174088912 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174088912 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/675 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174088912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088912 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 40, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 21, 21, 21, 49, 49, 49, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/676 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174088912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088912 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 21, 39, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174088912 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 Building ZINC000174088912 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174088912 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 675) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174088912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088912 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 40, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 21, 21, 21, 49, 49, 49, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 676) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1) `ZINC000174088912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174088912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174088912 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 21, 39, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174088912 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174088912 Building ZINC000174165978 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174165978 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/677 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174165978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165978 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 31, 31, 31, 31, 31, 42, 42, 42, 42, 31, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 31, 31, 31, 42, 42, 42, 31, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/678 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174165978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165978 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 36, 36, 36, 36, 36, 46, 46, 46, 46, 36, 5, 5, 5, 5, 5, 5, 5, 4, 7, 7, 7, 36, 36, 36, 46, 46, 46, 36, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174165978 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 Building ZINC000174165978 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174165978 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 677) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174165978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165978 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 31, 31, 31, 31, 31, 42, 42, 42, 42, 31, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 31, 31, 31, 42, 42, 42, 31, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 678) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174165978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165978 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 36, 36, 36, 36, 36, 46, 46, 46, 46, 36, 5, 5, 5, 5, 5, 5, 5, 4, 7, 7, 7, 36, 36, 36, 46, 46, 46, 36, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174165978 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165978 Building ZINC000174165989 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174165989 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/679 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174165989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165989 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 37, 37, 37, 37, 37, 47, 47, 47, 47, 37, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 37, 37, 37, 47, 47, 47, 37, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/680 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174165989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165989 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 31, 31, 31, 31, 31, 42, 42, 42, 42, 31, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 31, 31, 31, 42, 42, 42, 31, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174165989 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 Building ZINC000174165989 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174165989 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 679) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174165989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165989 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 37, 37, 37, 37, 37, 47, 47, 47, 47, 37, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 37, 37, 37, 47, 47, 47, 37, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 680) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1) `ZINC000174165989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174165989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174165989 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(n3cccn3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 31, 31, 31, 31, 31, 42, 42, 42, 42, 31, 6, 6, 6, 6, 6, 6, 6, 3, 6, 6, 6, 31, 31, 31, 42, 42, 42, 31, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174165989 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174165989 Building ZINC000174331328 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174331328 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/681 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1) `ZINC000174331328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174331328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331328 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 36, 50, 50, 36, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 17, 17, 17, 50, 50, 41, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/682 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1) `ZINC000174331328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174331328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331328 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 34, 47, 47, 41, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 18, 18, 18, 47, 47, 47, 47, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174331328 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 Building ZINC000174331328 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174331328 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 681) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1) `ZINC000174331328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174331328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331328 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 36, 50, 50, 36, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 17, 17, 17, 50, 50, 41, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 682) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1) `ZINC000174331328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174331328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331328 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 34, 47, 47, 41, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 18, 18, 18, 47, 47, 47, 47, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174331328 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331328 Building ZINC000174331342 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174331342 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/683 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1) `ZINC000174331342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174331342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331342 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 19, 34, 47, 47, 40, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 19, 19, 19, 47, 47, 41, 47, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/684 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1) `ZINC000174331342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174331342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331342 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 35, 50, 50, 39, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 16, 16, 16, 50, 50, 42, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174331342 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 Building ZINC000174331342 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174331342 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 683) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1) `ZINC000174331342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174331342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331342 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 19, 34, 47, 47, 40, 47, 47, 47, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 19, 19, 19, 47, 47, 41, 47, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 684) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1) `ZINC000174331342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174331342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174331342 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccccc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 35, 50, 50, 39, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 16, 16, 16, 50, 50, 42, 50, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174331342 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174331342 Building ZINC000494493560 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000494493560 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/685 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000494493560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000494493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000494493560 none CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 28, 28, 28, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 28, 28, 28, 36, 36, 36, 36, 36, 28, 12, 12, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/686 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000494493560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000494493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000494493560 none CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 29, 29, 29, 35, 35, 35, 35, 35, 29, 12, 12, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000494493560 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 Building ZINC000494493560 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000494493560 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 685) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000494493560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000494493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000494493560 none CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 28, 28, 28, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 28, 28, 28, 36, 36, 36, 36, 36, 28, 12, 12, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 686) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1) `ZINC000494493560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000494493560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000494493560 none CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 29, 29, 29, 35, 35, 35, 35, 35, 29, 12, 12, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000494493560 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000494493560 Building ZINC000908207744 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908207744 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/687 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908207744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207744 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 20, 20, 20, 22, 22, 22, 20, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 60, 22, 22, 22, 22] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/688 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908207744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207744 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 20, 20, 20, 23, 23, 20, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 60, 23, 23, 23, 23] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908207744 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 Building ZINC000908207744 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908207744 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 687) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908207744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207744 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 20, 20, 20, 22, 22, 22, 20, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 60, 22, 22, 22, 22] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 688) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908207744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207744 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 20, 20, 20, 23, 23, 20, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 60, 23, 23, 23, 23] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908207744 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207744 Building ZINC000908207745 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908207745 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/689 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908207745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207745 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 60, 20, 20, 20, 20] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/690 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908207745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207745 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 22, 22, 21, 21, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 63, 22, 22, 22, 22] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908207745 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 Building ZINC000908207745 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908207745 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 689) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908207745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207745 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 60, 20, 20, 20, 20] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 690) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1) `ZINC000908207745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908207745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908207745 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 22, 22, 21, 21, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 63, 22, 22, 22, 22] 150 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908207745 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908207745 Building ZINC000157156607 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000157156607 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/691 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Cl)cn2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157156607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000157156607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000157156607 none O=C(Nc1nc2ccc(Cl)cn2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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: [10, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 10, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12] 47 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/692 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Cl)cn2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157156607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000157156607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000157156607 none O=C(Nc1nc2ccc(Cl)cn2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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: [10, 1, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 10, 26, 26, 26, 12, 12, 12, 12, 12, 12, 12, 12, 12] 46 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000157156607 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 Building ZINC000157156607 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000157156607 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 691) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Cl)cn2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157156607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000157156607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000157156607 none O=C(Nc1nc2ccc(Cl)cn2n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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: [10, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 10, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12] 47 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 692) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Cl)cn2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157156607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000157156607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000157156607 none O=C(Nc1nc2ccc(Cl)cn2n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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: [10, 1, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 10, 26, 26, 26, 12, 12, 12, 12, 12, 12, 12, 12, 12] 46 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000157156607 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157156607 Building ZINC000174385713 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174385713 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/693 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385713 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 22, 22, 22, 42, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 22, 22, 22, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/694 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385713 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 21, 21, 21, 41, 48, 48, 45, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 21, 21, 21, 48, 48, 48, 48, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174385713 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 Building ZINC000174385713 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174385713 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 693) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385713 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 22, 22, 22, 42, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 22, 22, 22, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 694) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174385713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385713 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 21, 21, 21, 41, 48, 48, 45, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 21, 21, 21, 48, 48, 48, 48, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174385713 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385713 Building ZINC000174385724 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174385724 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/695 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174385724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385724 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 10, 20, 20, 20, 41, 48, 48, 47, 47, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 10, 10, 20, 20, 20, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/696 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174385724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385724 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 22, 22, 22, 41, 50, 50, 49, 49, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 22, 22, 22, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174385724 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 Building ZINC000174385724 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174385724 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 695) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174385724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385724 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 10, 20, 20, 20, 41, 48, 48, 47, 47, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 10, 10, 20, 20, 20, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 696) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1) `ZINC000174385724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174385724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000174385724 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 22, 22, 22, 41, 50, 50, 49, 49, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 22, 22, 22, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174385724 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174385724 Building ZINC000345789126 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000345789126 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/697 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)n2C) `ZINC000345789126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000345789126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000345789126 none Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 5, 4, 4, 4, 4, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/698 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)n2C) `ZINC000345789126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000345789126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000345789126 none Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 5, 4, 4, 4, 4, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000345789126 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 Building ZINC000345789126 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000345789126 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 697) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)n2C) `ZINC000345789126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000345789126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000345789126 none Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 5, 4, 4, 4, 4, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 698) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)n2C) `ZINC000345789126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000345789126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000345789126 none Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 5, 4, 4, 4, 4, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000345789126 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000345789126 Building ZINC000650160536 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650160536 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/699 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)CCC2)cn1) `ZINC000650160536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650160536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650160536 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 4, 4, 6, 10, 14, 14, 10, 14, 14, 14, 10, 10, 10, 8, 8, 24, 24, 24, 24, 24, 8, 4, 14, 14, 10, 14, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/700 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)CCC2)cn1) `ZINC000650160536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650160536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650160536 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 10, 13, 13, 10, 13, 13, 13, 10, 10, 10, 9, 9, 26, 26, 26, 26, 26, 9, 4, 13, 13, 10, 13, 10, 10, 10, 10, 10, 10, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650160536 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 Building ZINC000650160536 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650160536 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 699) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)CCC2)cn1) `ZINC000650160536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650160536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650160536 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 4, 4, 6, 10, 14, 14, 10, 14, 14, 14, 10, 10, 10, 8, 8, 24, 24, 24, 24, 24, 8, 4, 14, 14, 10, 14, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 700) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)CCC2)cn1) `ZINC000650160536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650160536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650160536 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', '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, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 10, 13, 13, 10, 13, 13, 13, 10, 10, 10, 9, 9, 26, 26, 26, 26, 26, 9, 4, 13, 13, 10, 13, 10, 10, 10, 10, 10, 10, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650160536 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650160536 Building ZINC000650164163 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650164163 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/701 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1) `ZINC000650164163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650164163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650164163 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 13, 21, 26, 26, 21, 26, 26, 26, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 26, 26, 21, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21] 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, 45, 46]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/702 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1) `ZINC000650164163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650164163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650164163 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 9, 9, 13, 23, 30, 30, 23, 30, 30, 30, 23, 23, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 30, 30, 23, 30, 30, 30, 30, 23, 23, 23, 23, 23, 23] 37 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650164163 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 Building ZINC000650164163 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650164163 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 701) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1) `ZINC000650164163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650164163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650164163 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 13, 21, 26, 26, 21, 26, 26, 26, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 26, 26, 21, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21] 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, 45, 46]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 702) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1) `ZINC000650164163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650164163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650164163 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccccc2C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 9, 9, 13, 23, 30, 30, 23, 30, 30, 30, 23, 23, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 30, 30, 23, 30, 30, 30, 30, 23, 23, 23, 23, 23, 23] 37 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650164163 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650164163 Building ZINC000650181117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000650181117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/703 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/704 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/705 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/705' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/706 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/706' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650181117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 Building ZINC000650181117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000650181117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 703) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 704) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 705) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 706) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650181117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 Building ZINC000650181117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000650181117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 703) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 704) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 705) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 706) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650181117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 Building ZINC000650181117 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000650181117 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 703) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 704) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 25, 25, 25, 25, 25, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 705) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 706) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl) `ZINC000650181117.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000650181117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650181117 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCN(C)CC(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 17, 21, 24, 24, 24, 24, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 12, 12, 21, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650181117 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650181117 Building ZINC000424108276 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424108276 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/707 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424108276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424108276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000424108276 none CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 50, 10, 26, 26, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 26, 27, 27, 27, 26, 10, 10, 10, 10, 2, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/708 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424108276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424108276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000424108276 none CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 50, 10, 26, 26, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 26, 27, 27, 27, 26, 10, 10, 10, 10, 2, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424108276 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 Building ZINC000424108276 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424108276 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 707) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424108276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424108276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000424108276 none CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 50, 10, 26, 26, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 26, 27, 27, 27, 26, 10, 10, 10, 10, 2, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 708) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424108276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424108276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000424108276 none CC(C)(C)OC(=O)C(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 50, 10, 26, 26, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 26, 27, 27, 27, 26, 10, 10, 10, 10, 2, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424108276 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424108276 Building ZINC000424115154 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424115154 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/709 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424115154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115154 none O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 23, 23, 23, 23, 14, 23, 33, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 2, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/710 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424115154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115154 none O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 20, 20, 20, 13, 20, 31, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424115154 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 Building ZINC000424115154 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424115154 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 709) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424115154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115154 none O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 23, 23, 23, 23, 14, 23, 33, 48, 48, 48, 48, 48, 1, 1, 1, 5, 5, 1, 2, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 200 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 710) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424115154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115154 none O=C(N1CC2(CCC2)[C@@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 20, 20, 20, 13, 20, 31, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424115154 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115154 Building ZINC000424115158 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424115158 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/711 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424115158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115158 none O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 20, 20, 20, 20, 20, 20, 29, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/712 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424115158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115158 none O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 22, 22, 22, 22, 22, 22, 22, 31, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424115158 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 Building ZINC000424115158 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424115158 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 711) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424115158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115158 none O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 20, 20, 20, 20, 20, 20, 20, 29, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 712) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000424115158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424115158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000424115158 none O=C(N1CC2(CCC2)[C@H]1C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 22, 22, 22, 22, 22, 22, 22, 31, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424115158 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424115158 Building ZINC000650204173 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650204173 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/713 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(nc1O)CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650204173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650204173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000650204173 none O=C(Nc1cc2c(nc1O)CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 19, 23, 23, 23, 19, 23, 23, 23, 23, 23, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 5, 23, 46, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/714 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(nc1O)CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650204173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650204173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000650204173 none O=C(Nc1cc2c(nc1O)CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 21, 28, 28, 28, 21, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 5, 28, 56, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650204173 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 Building ZINC000650204173 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650204173 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 713) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(nc1O)CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650204173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650204173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000650204173 none O=C(Nc1cc2c(nc1O)CCCC2)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 19, 23, 23, 23, 19, 23, 23, 23, 23, 23, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 5, 23, 46, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 714) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(nc1O)CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650204173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650204173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000650204173 none O=C(Nc1cc2c(nc1O)CCCC2)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 21, 28, 28, 28, 21, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 5, 28, 56, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650204173 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650204173 Building ZINC000650208062 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650208062 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/715 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2) `ZINC000650208062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650208062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650208062 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 41, 45, 45, 45, 41, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 11, 45, 90, 45, 45, 45, 45, 45, 45, 45, 45] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/716 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2) `ZINC000650208062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650208062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650208062 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 41, 45, 45, 45, 41, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 11, 45, 90, 45, 45, 45, 45, 45, 45, 45, 45] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650208062 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 Building ZINC000650208062 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650208062 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 715) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2) `ZINC000650208062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650208062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650208062 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 41, 45, 45, 45, 41, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 11, 45, 90, 45, 45, 45, 45, 45, 45, 45, 45] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 716) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2) `ZINC000650208062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650208062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650208062 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(nc1O)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 41, 45, 45, 45, 41, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 11, 45, 90, 45, 45, 45, 45, 45, 45, 45, 45] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650208062 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650208062 Building ZINC000650223629 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650223629 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/717 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/717' -> `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@](C)(c2cccc(F)c2)C1) `ZINC000650223629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650223629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223629 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 36, 36, 36, 36, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 58 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/718 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/718' -> `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@](C)(c2cccc(F)c2)C1) `ZINC000650223629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650223629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223629 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650223629 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 Building ZINC000650223629 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650223629 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 717) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@](C)(c2cccc(F)c2)C1) `ZINC000650223629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650223629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223629 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 36, 36, 36, 36, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 58 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 718) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@](C)(c2cccc(F)c2)C1) `ZINC000650223629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650223629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223629 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650223629 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223629 Building ZINC000650223630 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650223630 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/719 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/719' -> `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@@](C)(c2cccc(F)c2)C1) `ZINC000650223630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650223630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223630 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/720 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/720' -> `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@@](C)(c2cccc(F)c2)C1) `ZINC000650223630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650223630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223630 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 14, 37, 37, 37, 37, 37, 37, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 37, 37, 37, 37, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650223630 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 Building ZINC000650223630 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650223630 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 719) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](C)(c2cccc(F)c2)C1) `ZINC000650223630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650223630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223630 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 13, 39, 39, 39, 39, 39, 39, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 39, 39, 39, 39, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 720) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@](C)(c2cccc(F)c2)C1) `ZINC000650223630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650223630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650223630 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@](C)(c2cccc(F)c2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 14, 37, 37, 37, 37, 37, 37, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 37, 37, 37, 37, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650223630 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650223630 Building ZINC000562578871 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000562578871 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/721 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OC(F)F)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000562578871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000562578871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000562578871 none O=C(NCc1ccc(OC(F)F)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 10, 10, 10, 10, 27, 27, 27, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 27, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/722 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OC(F)F)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000562578871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000562578871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000562578871 none O=C(NCc1ccc(OC(F)F)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 10, 10, 10, 10, 27, 27, 27, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 27, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000562578871 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 Building ZINC000562578871 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000562578871 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 721) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OC(F)F)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000562578871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000562578871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000562578871 none O=C(NCc1ccc(OC(F)F)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 10, 10, 10, 10, 27, 27, 27, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 27, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 722) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OC(F)F)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000562578871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000562578871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000562578871 none O=C(NCc1ccc(OC(F)F)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 10, 10, 10, 10, 27, 27, 27, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 27, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000562578871 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000562578871 Building ZINC000650238859 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650238859 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/723 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1) `ZINC000650238859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650238859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650238859 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 2, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 8, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/724 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1) `ZINC000650238859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650238859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650238859 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 2, 8, 8, 8, 8, 20, 20, 20, 20, 20, 8, 8, 8, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650238859 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 Building ZINC000650238859 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650238859 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 723) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1) `ZINC000650238859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650238859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650238859 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 2, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 8, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 724) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1) `ZINC000650238859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650238859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650238859 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCc3oc(c4ccccc4)cc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 2, 8, 8, 8, 8, 20, 20, 20, 20, 20, 8, 8, 8, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650238859 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650238859 Building ZINC000926520778 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000926520778 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/725 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC000926520778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000926520778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000926520778 none COC(=O)[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [44, 44, 20, 44, 20, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 44, 44, 44, 20, 20, 20, 20, 4, 4, 1, 4, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/726 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC000926520778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000926520778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000926520778 none COC(=O)[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [45, 45, 23, 45, 23, 23, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 23, 45, 45, 45, 23, 23, 23, 23, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000926520778 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 Building ZINC000926520778 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000926520778 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 725) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC000926520778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000926520778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000926520778 none COC(=O)[C@@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [44, 44, 20, 44, 20, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 44, 44, 44, 20, 20, 20, 20, 4, 4, 1, 4, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 726) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC000926520778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000926520778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000926520778 none COC(=O)[C@@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [45, 45, 23, 45, 23, 23, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 23, 45, 45, 45, 23, 23, 23, 23, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000926520778 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926520778 Building ZINC000650298021 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650298021 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/727 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650298021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298021 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 10, 10, 10, 10, 10, 10, 16, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/728 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650298021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298021 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 13, 13, 19, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 31, 31, 31, 31, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650298021 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 Building ZINC000650298021 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650298021 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 727) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650298021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298021 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 10, 10, 10, 10, 10, 10, 16, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 728) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650298021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298021 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 13, 13, 19, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 31, 31, 31, 31, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650298021 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298021 Building ZINC000650298022 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650298022 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/729 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650298022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298022 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 13, 13, 19, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 31, 31, 31, 31, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/730 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650298022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298022 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 9, 15, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650298022 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 Building ZINC000650298022 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650298022 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 729) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650298022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298022 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 13, 13, 19, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 31, 31, 31, 31, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 730) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)c2)cn1) `ZINC000650298022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650298022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000650298022 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 9, 15, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650298022 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650298022 Building ZINC000650318193 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650318193 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/731 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650318193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650318193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000650318193 none O=C(N1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 18, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/732 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650318193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650318193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000650318193 none O=C(N1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 17, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 5, 5, 1, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5] 45 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650318193 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 Building ZINC000650318193 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650318193 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 731) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650318193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650318193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000650318193 none O=C(N1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 18, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 1, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 732) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650318193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650318193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000650318193 none O=C(N1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 17, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 5, 5, 1, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5] 45 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650318193 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650318193 Building ZINC000650353827 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650353827 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/733 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000650353827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650353827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000650353827 none O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/734 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000650353827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650353827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000650353827 none O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 24 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650353827 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 Building ZINC000650353827 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650353827 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 733) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000650353827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650353827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000650353827 none O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 734) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000650353827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650353827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000650353827 none O=C(N1CCC2(CC1)C(F)(F)C2(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 24 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650353827 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353827 Building ZINC000650353871 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650353871 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/735 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F) `ZINC000650353871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650353871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650353871 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 8, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23] 33 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/736 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F) `ZINC000650353871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650353871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650353871 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 10, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24] 38 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650353871 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 Building ZINC000650353871 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650353871 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 735) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F) `ZINC000650353871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650353871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650353871 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 8, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23] 33 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 736) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F) `ZINC000650353871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650353871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650353871 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)C(F)(F)C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 10, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24] 38 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650353871 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650353871 Building ZINC000650357979 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650357979 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/737 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1) `ZINC000650357979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650357979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650357979 none COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 16, 16, 16, 16, 6, 1, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 48, 48, 50, 50, 50, 48, 48, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/738 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1) `ZINC000650357979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650357979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650357979 none COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 46, 46, 50, 50, 50, 46, 46, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650357979 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 Building ZINC000650357979 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650357979 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 737) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1) `ZINC000650357979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650357979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650357979 none COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 16, 16, 16, 16, 6, 1, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 48, 48, 50, 50, 50, 48, 48, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 738) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1) `ZINC000650357979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650357979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650357979 none COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 46, 46, 50, 50, 50, 46, 46, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650357979 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650357979 Building ZINC000650358404 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650358404 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/739 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1) `ZINC000650358404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650358404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000650358404 none COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 46, 46, 46, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 46, 46, 50, 50, 50, 46, 46, 15, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/740 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1) `ZINC000650358404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650358404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000650358404 none COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 16, 16, 16, 16, 6, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 47, 47, 50, 50, 50, 47, 47, 16, 16, 16, 16, 16, 3, 3, 3, 3, 16, 16, 16, 16, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650358404 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 Building ZINC000650358404 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650358404 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 739) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1) `ZINC000650358404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650358404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000650358404 none COc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 46, 46, 46, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 46, 46, 50, 50, 50, 46, 46, 15, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15, 46] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 740) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1) `ZINC000650358404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650358404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000650358404 none COc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 16, 16, 16, 16, 6, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 47, 47, 50, 50, 50, 47, 47, 16, 16, 16, 16, 16, 3, 3, 3, 3, 16, 16, 16, 16, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650358404 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650358404 Building ZINC000650359106 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650359106 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/741 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650359106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359106 none O=C(NC[C@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 26, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/742 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650359106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359106 none O=C(NC[C@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 24, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 14, 14, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 305 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650359106 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 Building ZINC000650359106 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650359106 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 741) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650359106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359106 none O=C(NC[C@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 26, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 742) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650359106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359106 none O=C(NC[C@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 24, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 14, 14, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 305 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650359106 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359106 Building ZINC000650359107 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650359107 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/743 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650359107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359107 none O=C(NC[C@@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 25, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/744 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650359107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359107 none O=C(NC[C@@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 26, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650359107 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 Building ZINC000650359107 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650359107 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 743) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650359107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359107 none O=C(NC[C@@]1(CO)CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 25, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 744) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000650359107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650359107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000650359107 none O=C(NC[C@@]1(CO)CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 26, 47, 50, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 50, 50, 150, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650359107 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650359107 Building ZINC000650367686 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650367686 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/745 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650367686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367686 none CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 23, 23, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/746 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650367686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367686 none CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 31, 32, 21, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650367686 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 Building ZINC000650367686 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650367686 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 745) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650367686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367686 none CC[C@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 23, 23, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 746) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650367686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367686 none CC[C@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 31, 32, 21, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650367686 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367686 Building ZINC000650367687 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650367687 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/747 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650367687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367687 none CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 31, 21, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 21, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/748 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650367687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367687 none CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 23, 23, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650367687 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 Building ZINC000650367687 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650367687 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 747) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650367687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367687 none CC[C@@H](OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 31, 21, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 21, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 748) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1) `ZINC000650367687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650367687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000650367687 none CC[C@@H](OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 23, 23, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650367687 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650367687 Building ZINC000650373369 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650373369 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/749 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C) `ZINC000650373369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650373369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650373369 none Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 6, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/750 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C) `ZINC000650373369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650373369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650373369 none Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 6, 6, 6, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650373369 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 Building ZINC000650373369 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650373369 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 749) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C) `ZINC000650373369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650373369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650373369 none Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 6, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 750) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C) `ZINC000650373369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650373369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650373369 none Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 6, 6, 6, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650373369 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650373369 Building ZINC000280915137 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915137 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/751 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915137 none C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 47, 47, 31, 47, 47, 29, 21, 4, 21, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 29, 47, 47, 31, 47, 47, 29, 29, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/752 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915137 none C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 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, 28, 28, 28, 28, 28, 28, 28, 47, 47, 32, 47, 47, 28, 22, 4, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 28, 28, 28, 28, 47, 47, 30, 47, 47, 28, 28, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915137 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 Building ZINC000280915137 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915137 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 751) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915137 none C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 47, 47, 31, 47, 47, 29, 21, 4, 21, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 29, 47, 47, 31, 47, 47, 29, 29, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 752) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915137 none C[C@@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 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, 28, 28, 28, 28, 28, 28, 28, 47, 47, 32, 47, 47, 28, 22, 4, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 28, 28, 28, 28, 47, 47, 30, 47, 47, 28, 28, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915137 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915137 Building ZINC000280915138 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915138 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/753 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915138 none C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 22, 34, 34, 21, 15, 1, 15, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 21, 21, 6, 6, 12, 6, 6] 70 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/754 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915138 none C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 37, 37, 20, 37, 37, 20, 14, 1, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 20, 20, 6, 6, 12, 6, 6] 76 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915138 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 Building ZINC000280915138 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915138 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 753) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915138 none C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 22, 34, 34, 21, 15, 1, 15, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 21, 21, 6, 6, 12, 6, 6] 70 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 754) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915138 none C[C@@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 37, 37, 20, 37, 37, 20, 14, 1, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 20, 20, 6, 6, 12, 6, 6] 76 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915138 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915138 Building ZINC000280915140 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915140 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/755 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915140 none C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 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: [26, 26, 26, 26, 26, 26, 26, 26, 48, 48, 40, 48, 48, 26, 21, 3, 21, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 48, 48, 43, 48, 48, 26, 26, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/756 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915140 none C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 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: [30, 30, 30, 30, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 22, 3, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 30, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915140 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 Building ZINC000280915140 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915140 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 755) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915140 none C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 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: [26, 26, 26, 26, 26, 26, 26, 26, 48, 48, 40, 48, 48, 26, 21, 3, 21, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 48, 48, 43, 48, 48, 26, 26, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 756) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915140 none C[C@H]1CO[C@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 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: [30, 30, 30, 30, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 22, 3, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 30, 5, 5, 10, 5, 5] 100 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915140 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915140 Building ZINC000280915141 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915141 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/757 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915141 none C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 19, 36, 36, 19, 14, 1, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 19, 19, 19, 36, 36, 19, 36, 36, 19, 19, 6, 6, 12, 6, 6] 74 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/758 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915141 none C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 31, 31, 18, 31, 31, 18, 13, 1, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 31, 31, 18, 31, 31, 18, 18, 5, 5, 10, 5, 5] 64 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915141 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 Building ZINC000280915141 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000280915141 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 757) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000280915141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915141 none C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 19, 36, 36, 19, 14, 1, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 19, 19, 19, 36, 36, 19, 36, 36, 19, 19, 6, 6, 12, 6, 6] 74 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 758) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000280915141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000280915141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000280915141 none C[C@H]1CO[C@@H](c2ccccc2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7, 3, 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] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 31, 31, 18, 31, 31, 18, 13, 1, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 18, 18, 18, 18, 31, 31, 18, 31, 31, 18, 18, 5, 5, 10, 5, 5] 64 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000280915141 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000280915141 Building ZINC000926628812 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000926628812 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/759 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1) `ZINC000926628812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000926628812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000926628812 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 11, 45, 11, 11, 11, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/760 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1) `ZINC000926628812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000926628812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000926628812 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 11, 42, 11, 11, 11, 2, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000926628812 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 Building ZINC000926628812 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000926628812 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 759) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1) `ZINC000926628812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000926628812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000926628812 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 11, 45, 11, 11, 11, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 760) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1) `ZINC000926628812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000926628812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000926628812 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C1CC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 11, 42, 11, 11, 11, 2, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000926628812 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926628812 Building ZINC000926629826 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000926629826 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/761 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1) `ZINC000926629826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000926629826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000926629826 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 4, 5, 5, 5, 5, 16, 16, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/762 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1) `ZINC000926629826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000926629826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000926629826 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 4, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000926629826 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 Building ZINC000926629826 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000926629826 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 761) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1) `ZINC000926629826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000926629826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000926629826 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 4, 5, 5, 5, 5, 16, 16, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 762) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1) `ZINC000926629826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000926629826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000926629826 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)OC(C)(C)C)[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 4, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000926629826 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000926629826 Building ZINC000650451302 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650451302 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/763 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/763' -> `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)(C)c2ccc(F)cc21) `ZINC000650451302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650451302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650451302 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 19 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]) total number of confs: 32 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/764 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/764' -> `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)(C)c2ccc(F)cc21) `ZINC000650451302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650451302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650451302 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 8, 12, 12, 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, 12] 19 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]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650451302 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 Building ZINC000650451302 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650451302 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 763) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)c2ccc(F)cc21) `ZINC000650451302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650451302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650451302 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 19 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]) total number of confs: 32 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 764) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)c2ccc(F)cc21) `ZINC000650451302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650451302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650451302 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 8, 12, 12, 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, 12] 19 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]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650451302 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650451302 Building ZINC000650459798 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650459798 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/765 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650459798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459798 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 20, 20, 18, 28, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 4, 20, 20, 20, 20, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/766 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650459798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459798 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 19, 19, 16, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 4, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650459798 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 Building ZINC000650459798 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650459798 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 765) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650459798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459798 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 20, 20, 18, 28, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 4, 20, 20, 20, 20, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 766) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650459798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459798 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 19, 19, 16, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 4, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650459798 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459798 Building ZINC000650459799 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650459799 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/767 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650459799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459799 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 21, 21, 15, 28, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 4, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/768 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650459799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459799 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 16, 16, 11, 27, 27, 27, 27, 27, 1, 1, 1, 7, 7, 7, 7, 7, 4, 16, 16, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650459799 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 Building ZINC000650459799 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650459799 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 767) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650459799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459799 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 21, 21, 15, 28, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 4, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 768) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000650459799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650459799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000650459799 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 16, 16, 11, 27, 27, 27, 27, 27, 1, 1, 1, 7, 7, 7, 7, 7, 4, 16, 16, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650459799 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650459799 Building ZINC000650465298 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650465298 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/769 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650465298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465298 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 14, 14, 10, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/770 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650465298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465298 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 16, 16, 13, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650465298 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 Building ZINC000650465298 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650465298 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 769) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650465298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465298 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 14, 14, 10, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 770) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650465298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465298 none O=C(N[C@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 16, 16, 13, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650465298 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465298 Building ZINC000650465299 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650465299 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/771 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650465299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465299 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 13, 13, 10, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/772 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650465299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465299 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 15, 15, 10, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650465299 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 Building ZINC000650465299 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650465299 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 771) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650465299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465299 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 13, 13, 10, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 772) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000650465299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650465299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000650465299 none O=C(N[C@@H](C1CC1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 15, 15, 10, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650465299 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650465299 Building ZINC000650479727 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479727 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/773 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479727 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 26, 26, 26, 26, 13, 2, 15, 1, 1, 1, 4, 4, 2, 4, 4, 4, 26, 26, 26, 26, 26, 36, 36, 36, 36, 36, 26, 26, 4, 4, 4, 4, 26, 26, 26, 26, 26] 38 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]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/774 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479727 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 13, 2, 15, 1, 1, 1, 6, 6, 1, 1, 6, 6, 27, 27, 27, 27, 27, 42, 42, 42, 42, 42, 27, 27, 6, 6, 6, 6, 27, 27, 27, 27, 27] 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]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479727 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 Building ZINC000650479727 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479727 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 773) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479727 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 26, 26, 26, 26, 13, 2, 15, 1, 1, 1, 4, 4, 2, 4, 4, 4, 26, 26, 26, 26, 26, 36, 36, 36, 36, 36, 26, 26, 4, 4, 4, 4, 26, 26, 26, 26, 26] 38 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]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 774) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479727 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 13, 2, 15, 1, 1, 1, 6, 6, 1, 1, 6, 6, 27, 27, 27, 27, 27, 42, 42, 42, 42, 42, 27, 27, 6, 6, 6, 6, 27, 27, 27, 27, 27] 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]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479727 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479727 Building ZINC000650479728 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479728 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/775 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479728 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 15, 2, 15, 1, 1, 1, 4, 4, 2, 4, 4, 4, 21, 21, 21, 21, 21, 45, 45, 45, 45, 45, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21, 21] 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]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/776 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479728 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 17, 2, 17, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 44, 44, 44, 44, 44, 25, 25, 5, 5, 5, 5, 25, 25, 25, 25, 25] 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479728 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 Building ZINC000650479728 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479728 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 775) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479728 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 15, 2, 15, 1, 1, 1, 4, 4, 2, 4, 4, 4, 21, 21, 21, 21, 21, 45, 45, 45, 45, 45, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21, 21] 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]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 776) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1) `ZINC000650479728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479728 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 17, 2, 17, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 44, 44, 44, 44, 44, 25, 25, 5, 5, 5, 5, 25, 25, 25, 25, 25] 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479728 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479728 Building ZINC000650479729 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479729 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/777 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479729 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 14, 3, 14, 1, 1, 1, 5, 5, 1, 5, 5, 5, 21, 21, 21, 21, 21, 42, 42, 42, 42, 42, 21, 21, 5, 5, 5, 5, 21, 21, 21, 21, 21] 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/778 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479729 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 12, 2, 12, 1, 1, 1, 5, 5, 1, 5, 5, 5, 17, 17, 17, 17, 17, 41, 41, 41, 41, 41, 17, 17, 5, 5, 5, 5, 17, 17, 17, 17, 17] 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]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479729 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 Building ZINC000650479729 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479729 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 777) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479729 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 14, 3, 14, 1, 1, 1, 5, 5, 1, 5, 5, 5, 21, 21, 21, 21, 21, 42, 42, 42, 42, 42, 21, 21, 5, 5, 5, 5, 21, 21, 21, 21, 21] 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 778) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479729 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 12, 2, 12, 1, 1, 1, 5, 5, 1, 5, 5, 5, 17, 17, 17, 17, 17, 41, 41, 41, 41, 41, 17, 17, 5, 5, 5, 5, 17, 17, 17, 17, 17] 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]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479729 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479729 Building ZINC000650479730 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479730 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/779 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479730 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [38, 20, 20, 20, 20, 12, 2, 12, 1, 1, 1, 6, 6, 1, 6, 6, 6, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20] 47 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]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/780 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479730 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 22, 22, 22, 22, 14, 2, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 22, 22, 6, 6, 6, 6, 22, 22, 22, 22, 22] 46 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]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479730 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 Building ZINC000650479730 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650479730 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 779) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650479730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479730 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [38, 20, 20, 20, 20, 12, 2, 12, 1, 1, 1, 6, 6, 1, 6, 6, 6, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20] 47 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]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 780) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1) `ZINC000650479730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650479730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650479730 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)[C@H](C)CO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 22, 22, 22, 22, 14, 2, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 22, 22, 6, 6, 6, 6, 22, 22, 22, 22, 22] 46 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]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650479730 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650479730 Building ZINC000908250744 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908250744 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/781 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1) `ZINC000908250744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908250744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908250744 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 11, 12, 5, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/782 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1) `ZINC000908250744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908250744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908250744 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 11, 12, 5, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908250744 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 Building ZINC000908250744 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908250744 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 781) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1) `ZINC000908250744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908250744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908250744 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 11, 12, 5, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 782) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1) `ZINC000908250744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908250744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908250744 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(C(=O)OC)c(C(C)C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 11, 12, 5, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 21, 21, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000908250744 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000908250744 Building ZINC000615579813 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615579813 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/783 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000615579813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615579813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000615579813 none CC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 16, 32, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 4, 4, 1, 4, 4, 4, 32, 32, 32, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4] 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]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/784 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000615579813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615579813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000615579813 none CC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 17, 31, 17, 17, 17, 17, 17, 17, 11, 1, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 36 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: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000615579813 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 Building ZINC000615579813 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615579813 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 783) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000615579813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615579813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000615579813 none CC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 16, 32, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 4, 4, 1, 4, 4, 4, 32, 32, 32, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4] 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]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 784) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000615579813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615579813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000615579813 none CC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 17, 31, 17, 17, 17, 17, 17, 17, 11, 1, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 36 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: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000615579813 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000615579813 Building ZINC000911990801 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911990801 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/785 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C) `ZINC000911990801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911990801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990801 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 13, 7, 13, 7, 7, 7, 7, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 60 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/786 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C) `ZINC000911990801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911990801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990801 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 16, 8, 15, 8, 8, 8, 8, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 16, 16, 16, 15, 15, 15, 8, 8, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911990801 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 Building ZINC000911990801 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911990801 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 785) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C) `ZINC000911990801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911990801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990801 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 13, 7, 13, 7, 7, 7, 7, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 60 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 786) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C) `ZINC000911990801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911990801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990801 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 16, 8, 15, 8, 8, 8, 8, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 16, 16, 16, 15, 15, 15, 8, 8, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911990801 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990801 Building ZINC000911990803 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911990803 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/787 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C) `ZINC000911990803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911990803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990803 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 5, 9, 9, 9, 9, 16, 9, 15, 9, 5, 9, 9, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 16, 16, 16, 15, 15, 15, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/788 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C) `ZINC000911990803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911990803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990803 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 13, 7, 13, 7, 4, 7, 7, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911990803 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 Building ZINC000911990803 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911990803 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 787) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C) `ZINC000911990803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911990803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990803 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 5, 9, 9, 9, 9, 16, 9, 15, 9, 5, 9, 9, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 16, 16, 16, 15, 15, 15, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 788) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C) `ZINC000911990803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911990803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000911990803 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CC(OC)(OC)C2)[C@@H]1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 13, 7, 13, 7, 4, 7, 7, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000911990803 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000911990803 Building ZINC000650568641 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650568641 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/789 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1) `ZINC000650568641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650568641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650568641 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 19, 43, 43, 43, 43, 43, 43, 16, 16, 16, 16, 16, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 155 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/790 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1) `ZINC000650568641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650568641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650568641 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 21, 46, 46, 46, 46, 46, 46, 17, 17, 17, 17, 17, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 150 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650568641 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 Building ZINC000650568641 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650568641 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 789) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1) `ZINC000650568641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650568641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650568641 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 19, 43, 43, 43, 43, 43, 43, 16, 16, 16, 16, 16, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43] 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]) total number of confs: 155 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 790) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1) `ZINC000650568641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650568641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000650568641 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCCOC1 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', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 21, 46, 46, 46, 46, 46, 46, 17, 17, 17, 17, 17, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46] 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]) total number of confs: 150 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650568641 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650568641 Building ZINC000650582617 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650582617 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/791 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/791' -> `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)Nc1cc(C(F)F)ccc1F) `ZINC000650582617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650582617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650582617 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 21, 46, 46, 5, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 46, 15, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/792 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/792' -> `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)Nc1cc(C(F)F)ccc1F) `ZINC000650582617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650582617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650582617 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 21, 47, 47, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 47, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650582617 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 Building ZINC000650582617 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650582617 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 791) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)F)ccc1F) `ZINC000650582617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650582617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650582617 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 21, 46, 46, 5, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 46, 15, 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: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 792) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)F)ccc1F) `ZINC000650582617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650582617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000650582617 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)F)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 21, 21, 47, 47, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 47, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650582617 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650582617 Building ZINC000565009299 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565009299 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/793 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C) `ZINC000565009299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565009299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000565009299 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 41, 8, 41, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 46, 46, 46, 46, 46, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/794 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C) `ZINC000565009299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565009299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000565009299 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 32, 29, 6, 29, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 6, 6, 6] 37 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000565009299 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 Building ZINC000565009299 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565009299 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 793) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C) `ZINC000565009299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565009299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000565009299 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 41, 8, 41, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 46, 46, 46, 46, 46, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 794) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C) `ZINC000565009299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565009299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000565009299 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[C@@H]1C 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 32, 29, 6, 29, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 6, 6, 6] 37 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000565009299 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000565009299 Building ZINC000126424617 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000126424617 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/795 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1) `ZINC000126424617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000126424617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000126424617 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 4, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/796 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1) `ZINC000126424617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000126424617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000126424617 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 11, 17, 17, 17, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 17, 17, 17, 17, 32, 32, 32, 32, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000126424617 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 Building ZINC000126424617 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000126424617 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 795) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1) `ZINC000126424617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000126424617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000126424617 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 4, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 796) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1) `ZINC000126424617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000126424617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000126424617 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 11, 17, 17, 17, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 17, 17, 17, 17, 32, 32, 32, 32, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000126424617 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000126424617 Building ZINC000650651636 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650651636 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/797 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1) `ZINC000650651636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650651636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651636 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 17, 17, 16, 17, 17, 17, 3, 3, 9, 9, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 17, 17, 17, 17, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/798 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1) `ZINC000650651636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650651636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651636 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 6, 6, 6, 6, 6, 6, 6, 12, 17, 17, 15, 17, 17, 17, 4, 4, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650651636 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 Building ZINC000650651636 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650651636 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 797) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1) `ZINC000650651636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650651636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651636 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 17, 17, 16, 17, 17, 17, 3, 3, 9, 9, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 17, 17, 17, 17, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 798) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1) `ZINC000650651636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650651636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651636 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 6, 6, 6, 6, 6, 6, 6, 12, 17, 17, 15, 17, 17, 17, 4, 4, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650651636 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651636 Building ZINC000650651637 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650651637 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/799 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1) `ZINC000650651637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651637 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 5, 5, 5, 5, 5, 5, 5, 11, 16, 16, 14, 16, 16, 16, 4, 4, 11, 11, 11, 11, 11, 4, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/800 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1) `ZINC000650651637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651637 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 17, 17, 16, 17, 17, 17, 3, 3, 10, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 17, 17, 17, 17, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650651637 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 Building ZINC000650651637 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650651637 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 799) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1) `ZINC000650651637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651637 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 5, 5, 5, 5, 5, 5, 5, 11, 16, 16, 14, 16, 16, 16, 4, 4, 11, 11, 11, 11, 11, 4, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 800) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1) `ZINC000650651637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650651637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650651637 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2Cc2ccccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 15, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 17, 17, 16, 17, 17, 17, 3, 3, 10, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 17, 17, 17, 17, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650651637 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650651637 Building ZINC000616400761 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000616400761 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/801 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1CSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000616400761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000616400761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000616400761 none O=C(NCCC1CSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 34, 45, 45, 45, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 17, 17, 31, 31, 45, 45, 45, 45, 45, 3, 3, 3, 3] 50 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, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/802 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1CSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000616400761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000616400761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000616400761 none O=C(NCCC1CSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 37, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 17, 17, 34, 34, 47, 47, 47, 47, 47, 3, 3, 3, 3] 50 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, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000616400761 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 Building ZINC000616400761 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000616400761 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 801) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1CSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000616400761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000616400761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000616400761 none O=C(NCCC1CSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 34, 45, 45, 45, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 17, 17, 31, 31, 45, 45, 45, 45, 45, 3, 3, 3, 3] 50 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, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 802) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1CSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000616400761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000616400761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000616400761 none O=C(NCCC1CSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 37, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 17, 17, 34, 34, 47, 47, 47, 47, 47, 3, 3, 3, 3] 50 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, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000616400761 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000616400761 Building ZINC000650693196 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650693196 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/803 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21) `ZINC000650693196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650693196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650693196 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 5, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 2, 11, 18, 25, 25, 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, 25, 25] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/804 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21) `ZINC000650693196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650693196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650693196 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 5, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 2, 6, 6, 1, 1, 1, 2, 11, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650693196 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 Building ZINC000650693196 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650693196 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 803) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21) `ZINC000650693196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650693196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650693196 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 5, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 2, 11, 18, 25, 25, 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, 25, 25] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 804) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21) `ZINC000650693196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650693196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650693196 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2c(C)cc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 5, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 2, 6, 6, 1, 1, 1, 2, 11, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650693196 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650693196 Building ZINC000650695090 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650695090 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/805 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC000650695090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650695090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650695090 none Cc1cc(C)c2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [21, 21, 21, 21, 21, 21, 21, 21, 10, 2, 16, 1, 1, 1, 10, 10, 10, 10, 22, 22, 22, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 21, 21, 21, 21] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/806 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC000650695090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650695090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650695090 none Cc1cc(C)c2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 23, 23, 23, 23, 23, 23, 23, 11, 2, 18, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 23, 23, 23, 23] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650695090 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 Building ZINC000650695090 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650695090 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 805) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC000650695090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650695090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650695090 none Cc1cc(C)c2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [21, 21, 21, 21, 21, 21, 21, 21, 10, 2, 16, 1, 1, 1, 10, 10, 10, 10, 22, 22, 22, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 21, 21, 21, 21] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 806) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC000650695090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650695090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000650695090 none Cc1cc(C)c2c(c1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 23, 23, 23, 23, 23, 23, 23, 11, 2, 18, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 23, 23, 23, 23] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650695090 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650695090 Building ZINC000650697865 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650697865 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/807 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cc(F)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000650697865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650697865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650697865 none CN(C)c1cc(F)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 12, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/808 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000650697865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650697865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650697865 none CN(C)c1cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 12, 24, 24, 24, 24, 24, 24, 12, 12, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650697865 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 Building ZINC000650697865 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650697865 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 807) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cc(F)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000650697865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650697865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650697865 none CN(C)c1cc(F)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 12, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 808) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000650697865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650697865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650697865 none CN(C)c1cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 12, 24, 24, 24, 24, 24, 24, 12, 12, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650697865 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650697865 Building ZINC000157391534 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000157391534 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/809 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cccc(F)c21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157391534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000157391534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000157391534 none O=C(N1CCOc2cccc(F)c21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 2, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8] 31 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/810 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cccc(F)c21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157391534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000157391534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000157391534 none O=C(N1CCOc2cccc(F)c21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 2, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8] 30 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: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000157391534 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 Building ZINC000157391534 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000157391534 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 809) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cccc(F)c21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157391534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000157391534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000157391534 none O=C(N1CCOc2cccc(F)c21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 2, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8] 31 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 810) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cccc(F)c21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000157391534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000157391534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000157391534 none O=C(N1CCOc2cccc(F)c21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 2, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8] 30 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: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000157391534 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157391534 Building ZINC000786663818 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000786663818 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/811 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000786663818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000786663818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000786663818 none COC(=O)CCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 22, 50, 14, 7, 7, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 50, 50, 50, 22, 22, 14, 14, 2, 7, 7, 2, 2, 2, 2, 2, 7] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/812 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000786663818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000786663818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000786663818 none COC(=O)CCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 21, 50, 14, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 50, 50, 50, 21, 21, 14, 14, 2, 8, 8, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000786663818 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 Building ZINC000786663818 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000786663818 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 811) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000786663818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000786663818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000786663818 none COC(=O)CCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 22, 50, 14, 7, 7, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 50, 50, 50, 22, 22, 14, 14, 2, 7, 7, 2, 2, 2, 2, 2, 7] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 812) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000786663818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000786663818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000786663818 none COC(=O)CCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 21, 50, 14, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 50, 50, 50, 21, 21, 14, 14, 2, 8, 8, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000786663818 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000786663818 Building ZINC000650747019 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650747019 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/813 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl) `ZINC000650747019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747019 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 12, 12, 12, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/814 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl) `ZINC000650747019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747019 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 3, 6, 6, 1, 1, 1, 2, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 11, 11, 11, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650747019 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 Building ZINC000650747019 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650747019 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 813) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl) `ZINC000650747019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747019 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 12, 12, 12, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 814) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl) `ZINC000650747019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650747019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747019 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 3, 6, 6, 1, 1, 1, 2, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 11, 11, 11, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650747019 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747019 Building ZINC000650747020 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650747020 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/815 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl) `ZINC000650747020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650747020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747020 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 4, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 11, 11, 11, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/816 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl) `ZINC000650747020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650747020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747020 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 4, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 13, 13, 13, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650747020 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 Building ZINC000650747020 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650747020 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 815) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl) `ZINC000650747020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650747020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747020 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 4, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 11, 11, 11, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 816) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl) `ZINC000650747020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650747020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000650747020 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)OCC23CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 4, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 13, 13, 13, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/74215/xan-8058115.14/working/building/ZINC000650747020 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650747020 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650747020 Building ZINC000650778468 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650778468 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/817 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)cn1) `ZINC000650778468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650778468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650778468 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 9, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/818 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)cn1) `ZINC000650778468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650778468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650778468 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 11, 11, 1, 1, 1, 2, 9, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 16, 16, 16, 16, 16, 16, 11] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650778468 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 Building ZINC000650778468 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650778468 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 817) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)cn1) `ZINC000650778468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650778468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650778468 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 9, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 818) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)cn1) `ZINC000650778468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650778468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650778468 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 11, 11, 1, 1, 1, 2, 9, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 16, 16, 16, 16, 16, 16, 11] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650778468 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650778468 Building ZINC000080032364 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080032364 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/819 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080032364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032364 none CCO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 43, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 47, 48, 48, 48, 48, 44, 44, 44, 44, 44, 22, 22, 14, 14, 3, 2, 2, 4, 4, 4, 2, 2, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/820 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080032364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032364 none CCO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 21, 46, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 48, 48, 48, 48, 48, 46, 46, 46, 46, 46, 22, 22, 14, 14, 2, 3, 3, 5, 5, 5, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000080032364 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 Building ZINC000080032364 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080032364 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 819) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080032364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032364 none CCO[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 43, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 47, 48, 48, 48, 48, 44, 44, 44, 44, 44, 22, 22, 14, 14, 3, 2, 2, 4, 4, 4, 2, 2, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 820) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080032364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032364 none CCO[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 21, 46, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 48, 48, 48, 48, 48, 46, 46, 46, 46, 46, 22, 22, 14, 14, 2, 3, 3, 5, 5, 5, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000080032364 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032364 Building ZINC000080032369 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080032369 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/821 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080032369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032369 none CCO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 20, 42, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 45, 46, 46, 46, 46, 42, 42, 42, 42, 42, 20, 20, 13, 13, 2, 3, 3, 5, 5, 5, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/822 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080032369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032369 none CCO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 21, 41, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 46, 49, 49, 49, 49, 42, 42, 42, 42, 42, 22, 22, 14, 14, 3, 2, 2, 4, 4, 4, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000080032369 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 Building ZINC000080032369 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000080032369 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 821) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000080032369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032369 none CCO[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 20, 42, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 45, 46, 46, 46, 46, 42, 42, 42, 42, 42, 20, 20, 13, 13, 2, 3, 3, 5, 5, 5, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 822) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1) `ZINC000080032369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000080032369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000080032369 none CCO[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 21, 41, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 46, 49, 49, 49, 49, 42, 42, 42, 42, 42, 22, 22, 14, 14, 3, 2, 2, 4, 4, 4, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000080032369 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000080032369 Building ZINC000617379778 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617379778 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/823 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/823' -> `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(c3ccco3)CC2)cn1) `ZINC000617379778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617379778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000617379778 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccco3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 31, 31, 31, 31, 10, 10, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 10, 10, 10, 31, 31, 31, 10, 10, 10, 10, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/824 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/824' -> `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(c3ccco3)CC2)cn1) `ZINC000617379778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617379778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000617379778 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccco3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 35, 35, 35, 35, 8, 8, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 8, 8, 8, 8, 8, 35, 35, 35, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000617379778 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 Building ZINC000617379778 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617379778 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 823) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccco3)CC2)cn1) `ZINC000617379778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617379778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000617379778 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccco3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 31, 31, 31, 31, 10, 10, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 10, 10, 10, 31, 31, 31, 10, 10, 10, 10, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 824) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccco3)CC2)cn1) `ZINC000617379778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617379778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000617379778 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccco3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 35, 35, 35, 35, 8, 8, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 8, 8, 8, 8, 8, 35, 35, 35, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000617379778 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617379778 Building ZINC000650798248 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650798248 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/825 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650798248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798248 none C[C@@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 34, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 5, 5, 14, 14, 34, 34, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/826 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650798248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798248 none C[C@@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 21, 31, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 16, 16, 31, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650798248 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 Building ZINC000650798248 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650798248 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 825) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650798248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798248 none C[C@@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 34, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 5, 5, 14, 14, 34, 34, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 826) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650798248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798248 none C[C@@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 21, 31, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 16, 16, 31, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650798248 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798248 Building ZINC000650798249 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650798249 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/827 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650798249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798249 none C[C@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 20, 30, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 5, 5, 15, 15, 30, 30, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/828 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650798249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798249 none C[C@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 23, 36, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 15, 15, 36, 36, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650798249 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 Building ZINC000650798249 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650798249 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 827) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650798249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798249 none C[C@H](COCC1CC1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 20, 30, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 5, 5, 15, 15, 30, 30, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 828) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650798249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650798249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000650798249 none C[C@H](COCC1CC1)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 23, 36, 50, 50, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 15, 15, 36, 36, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650798249 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650798249 Building ZINC000158628046 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158628046 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/829 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1) `ZINC000158628046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158628046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000158628046 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 2, 11, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11] 35 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/830 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1) `ZINC000158628046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158628046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000158628046 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 1, 10, 10, 1, 1, 1, 2, 11, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 10, 10] 36 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158628046 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 Building ZINC000158628046 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158628046 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 829) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1) `ZINC000158628046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158628046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000158628046 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 2, 11, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11] 35 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 830) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1) `ZINC000158628046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158628046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000158628046 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCOc3c(Cl)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 1, 10, 10, 1, 1, 1, 2, 11, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 10, 10] 36 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158628046 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158628046 Building ZINC000157565187 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000157565187 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/831 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2nc(CNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21) `ZINC000157565187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000157565187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000157565187 none Cc1cccc2nc(CNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/832 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2nc(CNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21) `ZINC000157565187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000157565187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000157565187 none Cc1cccc2nc(CNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000157565187 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 Building ZINC000157565187 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000157565187 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 831) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2nc(CNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21) `ZINC000157565187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000157565187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000157565187 none Cc1cccc2nc(CNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 832) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2nc(CNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21) `ZINC000157565187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000157565187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000157565187 none Cc1cccc2nc(CNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)n(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000157565187 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000157565187 Building ZINC000617986468 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617986468 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/833 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CCC2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000617986468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617986468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000617986468 none COCC1(C2CCC2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 10, 10, 10, 25, 25, 25, 10, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 10, 28, 28, 28, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 3, 3, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/834 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CCC2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000617986468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617986468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000617986468 none COCC1(C2CCC2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 10, 24, 24, 24, 10, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 30, 30, 30, 25, 25, 24, 24, 24, 24, 24, 24, 24, 10, 10, 4, 4, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000617986468 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 Building ZINC000617986468 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617986468 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 833) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CCC2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000617986468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617986468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000617986468 none COCC1(C2CCC2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 10, 10, 10, 25, 25, 25, 10, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 10, 28, 28, 28, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 3, 3, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 834) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CCC2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000617986468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617986468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000617986468 none COCC1(C2CCC2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 10, 10, 24, 24, 24, 10, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 30, 30, 30, 25, 25, 24, 24, 24, 24, 24, 24, 24, 10, 10, 4, 4, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000617986468 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000617986468 Building ZINC000424877133 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424877133 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/835 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1) `ZINC000424877133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424877133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000424877133 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 42, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/836 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1) `ZINC000424877133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424877133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000424877133 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 43, 50, 50, 50, 50, 50, 50, 50, 10, 10, 3, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424877133 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 Building ZINC000424877133 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424877133 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 835) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1) `ZINC000424877133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424877133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000424877133 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 42, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 836) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1) `ZINC000424877133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424877133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000424877133 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 43, 50, 50, 50, 50, 50, 50, 50, 10, 10, 3, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424877133 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424877133 Building ZINC000424946397 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424946397 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/837 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/837' -> `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])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424946397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946397 none CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 28, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 48, 48, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/838 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/838' -> `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])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424946397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946397 none CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 15, 8, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 46, 46, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 2, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424946397 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 Building ZINC000424946397 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424946397 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 837) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424946397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946397 none CC(C)C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 28, 28, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 48, 48, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 838) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424946397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946397 none CC(C)C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 15, 8, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 46, 46, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 2, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424946397 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946397 Building ZINC000424946398 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424946398 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/839 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/839' -> `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])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424946398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946398 none CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 18, 12, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 47, 47, 48, 48, 48, 48, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/840 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/840' -> `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])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424946398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946398 none CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 25, 15, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 48, 48, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424946398 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 Building ZINC000424946398 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000424946398 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 839) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000424946398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946398 none CC(C)C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 18, 12, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 47, 47, 48, 48, 48, 48, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 840) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000424946398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000424946398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000424946398 none CC(C)C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 25, 15, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 48, 48, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 3, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000424946398 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000424946398 Building ZINC000425012275 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012275 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/841 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012275 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 21, 21, 16, 21, 21, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 4, 14, 14, 21, 21, 16, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/842 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012275 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 23, 23, 14, 23, 23, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 14, 14, 23, 23, 14, 23, 23, 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, 42, 43]) total number of confs: 120 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012275 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 Building ZINC000425012275 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012275 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 841) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012275 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 21, 21, 16, 21, 21, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 4, 14, 14, 21, 21, 16, 21, 21, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 842) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012275 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 23, 23, 14, 23, 23, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 14, 14, 23, 23, 14, 23, 23, 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, 42, 43]) total number of confs: 120 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012275 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012275 Building ZINC000425012276 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012276 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/843 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012276 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 19, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 21, 13, 21, 21, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 4, 13, 13, 21, 21, 13, 21, 21, 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, 42, 43]) total number of confs: 122 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/844 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012276 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 22, 22, 14, 22, 22, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 14, 14, 22, 22, 14, 22, 22, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012276 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 Building ZINC000425012276 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012276 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 843) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012276 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 19, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 21, 13, 21, 21, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 4, 13, 13, 21, 21, 13, 21, 21, 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, 42, 43]) total number of confs: 122 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 844) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012276 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 22, 22, 14, 22, 22, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 14, 14, 22, 22, 14, 22, 22, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012276 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012276 Building ZINC000425012277 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012277 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/845 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012277 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 7, 7, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 24, 24, 14, 24, 24, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 4, 14, 14, 24, 24, 14, 24, 24, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/846 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012277 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 22, 22, 12, 22, 22, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 12, 12, 22, 22, 12, 22, 22, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012277 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 Building ZINC000425012277 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012277 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 845) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012277 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 7, 7, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 24, 24, 14, 24, 24, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 4, 14, 14, 24, 24, 14, 24, 24, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 846) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1) `ZINC000425012277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012277 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 22, 22, 12, 22, 22, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 12, 12, 22, 22, 12, 22, 22, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012277 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012277 Building ZINC000425012278 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012278 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/847 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012278 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 13, 13, 22, 22, 22, 22, 22, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/848 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012278 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 7, 7, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 4, 13, 13, 25, 25, 25, 25, 25, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012278 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 Building ZINC000425012278 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425012278 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 847) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425012278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012278 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 13, 13, 22, 22, 22, 22, 22, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 848) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1) `ZINC000425012278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425012278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425012278 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@]2(F)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 7, 7, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 4, 13, 13, 25, 25, 25, 25, 25, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425012278 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425012278 Building ZINC000650850840 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650850840 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/849 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)cn1) `ZINC000650850840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650850840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650850840 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 11, 11, 1, 1, 1, 2, 11, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 21, 21, 21, 21, 21, 21, 11] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/850 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)cn1) `ZINC000650850840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650850840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650850840 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 10, 10, 1, 1, 1, 2, 11, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650850840 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 Building ZINC000650850840 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650850840 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 849) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)cn1) `ZINC000650850840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650850840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650850840 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 16, 16, 11, 11, 1, 1, 1, 2, 11, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 21, 21, 21, 21, 21, 21, 11] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 850) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)cn1) `ZINC000650850840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650850840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000650850840 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCOc3c(F)cc(F)cc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 10, 10, 1, 1, 1, 2, 11, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650850840 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650850840 Building ZINC000425027894 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425027894 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/851 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425027894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027894 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 5, 20, 20, 46, 46, 46, 4, 5, 8, 12, 12, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 20, 20, 20, 46, 46, 46, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/852 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425027894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027894 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 4, 15, 15, 41, 41, 41, 3, 4, 8, 13, 13, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 15, 15, 15, 41, 41, 41, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425027894 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 Building ZINC000425027894 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425027894 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 851) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425027894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027894 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 5, 20, 20, 46, 46, 46, 4, 5, 8, 12, 12, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 20, 20, 20, 46, 46, 46, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 852) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425027894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027894 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 4, 15, 15, 41, 41, 41, 3, 4, 8, 13, 13, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 15, 15, 15, 41, 41, 41, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425027894 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027894 Building ZINC000425027896 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425027896 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/853 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425027896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027896 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 5, 19, 19, 44, 44, 44, 4, 5, 8, 12, 12, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 24, 24, 19, 19, 19, 44, 44, 44, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/854 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425027896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027896 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 5, 20, 20, 45, 45, 45, 4, 5, 8, 13, 13, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 20, 20, 20, 45, 45, 45, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425027896 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 Building ZINC000425027896 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425027896 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 853) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425027896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027896 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 5, 19, 19, 44, 44, 44, 4, 5, 8, 12, 12, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 24, 24, 19, 19, 19, 44, 44, 44, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 223 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 854) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000425027896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425027896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425027896 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 5, 20, 20, 45, 45, 45, 4, 5, 8, 13, 13, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 20, 20, 20, 45, 45, 45, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 240 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425027896 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425027896 Building ZINC000425031357 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031357 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/855 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031357 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 45, 45, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/856 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031357 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031357 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 Building ZINC000425031357 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031357 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 855) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031357 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 45, 45, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 856) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031357 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031357 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031357 Building ZINC000425031358 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031358 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/857 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031358 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 12, 12, 45, 45, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/858 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031358 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031358 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 Building ZINC000425031358 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031358 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 857) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031358 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 12, 12, 45, 45, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 858) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031358 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031358 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031358 Building ZINC000425031359 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031359 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/859 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031359 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 43, 43, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/860 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031359 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 42, 42, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031359 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 Building ZINC000425031359 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031359 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 859) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031359 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 43, 43, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 860) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425031359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031359 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 42, 42, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031359 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031359 Building ZINC000425031360 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031360 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/861 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031360 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 10, 3, 10, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 14, 45, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/862 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031360 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 4, 3, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 38, 38, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031360 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 Building ZINC000425031360 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031360 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 861) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031360 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 10, 3, 10, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 14, 45, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 862) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425031360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425031360 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 4, 3, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 38, 38, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031360 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031360 Building ZINC000425031639 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031639 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/863 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000425031639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000425031639 none COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 22, 36, 36, 36, 15, 6, 15, 15, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 15, 6, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 139 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/864 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000425031639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000425031639 none COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 36, 36, 16, 7, 16, 16, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031639 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 Building ZINC000425031639 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425031639 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 863) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000425031639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425031639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000425031639 none COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 22, 36, 36, 36, 15, 6, 15, 15, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15, 15, 15, 6, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 139 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 864) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000425031639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425031639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000425031639 none COc1ccc(Cl)cc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 36, 36, 16, 7, 16, 16, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425031639 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425031639 Building ZINC000425035103 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035103 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/865 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035103 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 43, 43, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/866 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035103 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035103 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 Building ZINC000425035103 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035103 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 865) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035103 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 43, 43, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 866) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035103 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035103 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035103 Building ZINC000425035104 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035104 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/867 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035104 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 7, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/868 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035104 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 8, 1, 1, 1, 2, 2, 1, 2, 2, 11, 11, 11, 42, 42, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035104 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 Building ZINC000425035104 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035104 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 867) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035104 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 7, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 868) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035104 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 8, 1, 1, 1, 2, 2, 1, 2, 2, 11, 11, 11, 42, 42, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035104 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035104 Building ZINC000425035105 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035105 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/869 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035105 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 46, 46, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/870 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035105 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 44, 44, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 2, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035105 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 Building ZINC000425035105 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035105 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 869) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035105 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 46, 46, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 870) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425035105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035105 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 44, 44, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 2, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035105 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035105 Building ZINC000425035106 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035106 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/871 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035106 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 10, 3, 10, 1, 1, 1, 2, 2, 1, 2, 2, 14, 14, 14, 45, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/872 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035106 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 4, 3, 4, 1, 1, 1, 3, 3, 1, 3, 3, 7, 7, 7, 37, 37, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035106 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 Building ZINC000425035106 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425035106 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 871) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035106 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 10, 3, 10, 1, 1, 1, 2, 2, 1, 2, 2, 14, 14, 14, 45, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 872) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425035106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425035106 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 4, 3, 4, 1, 1, 1, 3, 3, 1, 3, 3, 7, 7, 7, 37, 37, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425035106 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425035106 Building ZINC000425041553 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041553 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/873 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041553 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/874 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041553 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 44, 44, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041553 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 Building ZINC000425041553 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041553 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 873) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041553 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 874) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041553 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 44, 44, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041553 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041553 Building ZINC000425041555 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041555 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/875 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041555 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/876 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041555 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 3, 11, 11, 11, 46, 46, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041555 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 Building ZINC000425041555 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041555 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 875) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041555 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 45, 45, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 876) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041555 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 3, 11, 11, 11, 46, 46, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041555 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041555 Building ZINC000425041558 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041558 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/877 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041558 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 43, 43, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/878 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041558 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041558 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 Building ZINC000425041558 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041558 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 877) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041558 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 43, 43, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 878) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C) `ZINC000425041558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041558 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041558 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041558 Building ZINC000425041561 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041561 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/879 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041561 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 14, 14, 10, 3, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 45, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/880 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041561 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 7, 4, 3, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 38, 38, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041561 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 Building ZINC000425041561 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041561 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 879) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041561 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 14, 14, 10, 3, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 45, 45, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 880) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C) `ZINC000425041561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000425041561 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H]1C(=O)OC(C)(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 7, 4, 3, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 38, 38, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 6, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041561 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041561 Building ZINC000425041845 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041845 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/881 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1) `ZINC000425041845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000425041845 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 7, 14, 14, 14, 14, 6, 6, 11, 11, 11, 11, 11, 6, 3, 7, 7, 7, 7, 7, 7, 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, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/882 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1) `ZINC000425041845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000425041845 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 9, 14, 14, 14, 14, 6, 6, 11, 11, 11, 11, 11, 6, 3, 7, 7, 7, 7, 7, 7, 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, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041845 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 Building ZINC000425041845 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425041845 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 881) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1) `ZINC000425041845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425041845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000425041845 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 7, 14, 14, 14, 14, 6, 6, 11, 11, 11, 11, 11, 6, 3, 7, 7, 7, 7, 7, 7, 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, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 882) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1) `ZINC000425041845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425041845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000425041845 none CCn1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)c2cc(Cl)ccc2OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 9, 14, 14, 14, 14, 6, 6, 11, 11, 11, 11, 11, 6, 3, 7, 7, 7, 7, 7, 7, 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, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425041845 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425041845 Building ZINC000425058384 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425058384 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/883 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(COCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000425058384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425058384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425058384 none O=C(Nc1ccc(COCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 2, 15, 28, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 15, 15, 28, 28, 28, 28, 84, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/884 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(COCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000425058384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425058384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425058384 none O=C(Nc1ccc(COCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 4, 15, 28, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 15, 15, 28, 28, 28, 28, 84, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425058384 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 Building ZINC000425058384 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425058384 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 883) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(COCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000425058384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425058384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425058384 none O=C(Nc1ccc(COCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 2, 15, 28, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 15, 15, 28, 28, 28, 28, 84, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 884) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(COCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000425058384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425058384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425058384 none O=C(Nc1ccc(COCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 4, 15, 28, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 15, 15, 28, 28, 28, 28, 84, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425058384 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425058384 Building ZINC000425084832 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084832 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/885 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084832 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 20, 20, 46, 46, 46, 2, 3, 7, 10, 10, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 20, 20, 20, 46, 46, 46, 7, 7, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/886 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084832 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 3, 15, 15, 39, 39, 39, 2, 3, 6, 10, 10, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 15, 15, 15, 39, 39, 39, 6, 6, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084832 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 Building ZINC000425084832 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084832 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 885) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084832 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 20, 20, 46, 46, 46, 2, 3, 7, 10, 10, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 20, 20, 20, 46, 46, 46, 7, 7, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 886) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084832 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 3, 15, 15, 39, 39, 39, 2, 3, 6, 10, 10, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 15, 15, 15, 39, 39, 39, 6, 6, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 182 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084832 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084832 Building ZINC000425084835 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084835 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/887 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084835 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 3, 19, 19, 46, 46, 46, 2, 3, 5, 9, 9, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 19, 19, 19, 46, 46, 46, 5, 5, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/888 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084835 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 2, 13, 13, 39, 39, 39, 2, 2, 5, 11, 11, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 13, 13, 13, 39, 39, 39, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084835 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 Building ZINC000425084835 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084835 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 887) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084835 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 3, 19, 19, 46, 46, 46, 2, 3, 5, 9, 9, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 19, 19, 19, 46, 46, 46, 5, 5, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 888) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC000425084835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000425084835 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 2, 13, 13, 39, 39, 39, 2, 2, 5, 11, 11, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 13, 13, 13, 39, 39, 39, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084835 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084835 Building ZINC000425086545 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425086545 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/889 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1) `ZINC000425086545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425086545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425086545 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 15, 26, 26, 4, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 4, 4, 15, 15, 26, 4, 4] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/890 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1) `ZINC000425086545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425086545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425086545 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 16, 32, 32, 4, 3, 3, 3, 7, 7, 4, 7, 7, 3, 3, 3, 4, 4, 4, 16, 16, 32, 4, 4] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 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: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425086545 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 Building ZINC000425086545 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425086545 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 889) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1) `ZINC000425086545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425086545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425086545 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 15, 26, 26, 4, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 4, 4, 15, 15, 26, 4, 4] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 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: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 890) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1) `ZINC000425086545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425086545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000425086545 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 16, 32, 32, 4, 3, 3, 3, 7, 7, 4, 7, 7, 3, 3, 3, 4, 4, 4, 16, 16, 32, 4, 4] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 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: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425086545 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425086545 Building ZINC000425087224 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425087224 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/891 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000425087224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425087224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000425087224 none O=C(N1CC(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 17, 17, 17, 42, 50, 50, 17, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 42, 42, 50, 17, 17, 3, 3, 3, 3] 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/892 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000425087224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425087224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000425087224 none O=C(N1CC(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 16, 16, 16, 41, 50, 50, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 16, 16, 41, 41, 50, 16, 16, 3, 3, 3, 3] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425087224 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 Building ZINC000425087224 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425087224 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 891) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000425087224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425087224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000425087224 none O=C(N1CC(CC(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 17, 17, 17, 42, 50, 50, 17, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 42, 42, 50, 17, 17, 3, 3, 3, 3] 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 892) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000425087224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425087224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000425087224 none O=C(N1CC(CC(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 16, 16, 16, 41, 50, 50, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 16, 16, 16, 41, 41, 50, 16, 16, 3, 3, 3, 3] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425087224 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425087224 Building ZINC000425084920 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084920 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/893 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084920 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 5, 21, 21, 45, 45, 45, 4, 5, 8, 12, 12, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 27, 27, 27, 21, 21, 21, 45, 45, 45, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/894 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084920 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 5, 21, 21, 46, 46, 46, 4, 5, 8, 13, 13, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 21, 21, 21, 46, 46, 46, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084920 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 Building ZINC000425084920 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084920 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 893) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084920 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 5, 21, 21, 45, 45, 45, 4, 5, 8, 12, 12, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 27, 27, 27, 21, 21, 21, 45, 45, 45, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 894) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084920 none CC[C@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 5, 21, 21, 46, 46, 46, 4, 5, 8, 13, 13, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 21, 21, 21, 46, 46, 46, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084920 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084920 Building ZINC000425084922 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084922 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/895 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084922 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 5, 21, 21, 46, 46, 46, 4, 5, 8, 13, 13, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 21, 21, 21, 46, 46, 46, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/896 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084922 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 4, 16, 16, 42, 42, 42, 3, 4, 8, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 16, 16, 16, 42, 42, 42, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084922 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 Building ZINC000425084922 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425084922 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 895) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425084922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084922 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 5, 21, 21, 46, 46, 46, 4, 5, 8, 13, 13, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 21, 21, 21, 46, 46, 46, 8, 8, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 896) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425084922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425084922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425084922 none CC[C@@](C)(C(=O)OC)N(CC1CC1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 12, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 4, 16, 16, 42, 42, 42, 3, 4, 8, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 16, 16, 16, 42, 42, 42, 8, 8, 12, 12, 12, 12, 12, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425084922 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425084922 Building ZINC000425119230 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425119230 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/897 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000425119230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425119230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000425119230 none COCc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 9, 9, 9, 2, 4, 4, 4, 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, 39, 40]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/898 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000425119230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425119230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000425119230 none COCc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 9, 9, 9, 3, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 31, 31, 9, 9, 9, 2, 4, 4, 4, 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, 39, 40]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425119230 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 Building ZINC000425119230 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425119230 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 897) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000425119230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425119230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000425119230 none COCc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 9, 9, 9, 2, 4, 4, 4, 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, 39, 40]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 898) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000425119230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425119230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000425119230 none COCc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 9, 9, 9, 3, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 31, 31, 9, 9, 9, 2, 4, 4, 4, 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, 39, 40]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425119230 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425119230 Building ZINC000521870460 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521870460 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/899 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOC(C)(C)C) `ZINC000521870460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521870460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000521870460 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 27, 41, 41, 41, 41, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 17, 17, 27, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/900 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOC(C)(C)C) `ZINC000521870460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521870460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000521870460 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 16, 26, 40, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 16, 16, 26, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000521870460 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 Building ZINC000521870460 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521870460 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 899) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOC(C)(C)C) `ZINC000521870460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521870460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000521870460 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCOC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 27, 41, 41, 41, 41, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 17, 17, 27, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 900) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOC(C)(C)C) `ZINC000521870460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521870460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000521870460 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCOC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 16, 26, 40, 41, 41, 41, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 16, 16, 26, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000521870460 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000521870460 Building ZINC000438983822 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438983822 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/901 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)c1nc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1) `ZINC000438983822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000438983822 none CO[C@@H](C)c1nc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 30, 30, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 30, 30, 30, 30, 30, 30, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24] 50 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/902 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)c1nc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1) `ZINC000438983822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000438983822 none CO[C@@H](C)c1nc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 28, 28, 28, 28, 28, 28, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 22] 50 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000438983822 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 Building ZINC000438983822 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438983822 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 901) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)c1nc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1) `ZINC000438983822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000438983822 none CO[C@@H](C)c1nc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 30, 30, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 30, 30, 30, 30, 30, 30, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24] 50 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 902) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)c1nc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1) `ZINC000438983822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000438983822 none CO[C@@H](C)c1nc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 28, 28, 28, 28, 28, 28, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 22] 50 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000438983822 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000438983822 Building ZINC000522006482 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522006482 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/903 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)O[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000522006482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522006482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000522006482 none CC(C)O[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 43, 48, 19, 19, 19, 19, 19, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 48, 48, 48, 48, 48, 48, 48, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19] 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: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/904 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)O[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000522006482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522006482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000522006482 none CC(C)O[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 39, 48, 18, 18, 18, 18, 18, 4, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 3, 3, 18, 18] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000522006482 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 Building ZINC000522006482 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522006482 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 903) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)O[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000522006482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522006482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000522006482 none CC(C)O[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 43, 48, 19, 19, 19, 19, 19, 4, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 48, 48, 48, 48, 48, 48, 48, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19] 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: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 904) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)O[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000522006482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522006482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000522006482 none CC(C)O[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 39, 48, 18, 18, 18, 18, 18, 4, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 3, 3, 3, 18, 18] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000522006482 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522006482 Building ZINC000804476034 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476034 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/905 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476034 none Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 32, 32, 29, 14, 29, 29, 4, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 87, 14, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/906 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476034 none Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 28, 26, 13, 26, 26, 3, 13, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 78, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476034 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 Building ZINC000804476034 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476034 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 905) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476034 none Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 32, 32, 29, 14, 29, 29, 4, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 87, 14, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 906) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476034 none Cc1ccc([C@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 28, 26, 13, 26, 26, 3, 13, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 78, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476034 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476034 Building ZINC000804476035 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476035 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/907 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476035 none Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 29, 29, 28, 10, 28, 28, 3, 10, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 84, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/908 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476035 none Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 11, 22, 22, 4, 11, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 66, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476035 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 Building ZINC000804476035 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476035 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 907) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476035 none Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 29, 29, 28, 10, 28, 28, 3, 10, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 84, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 908) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476035 none Cc1ccc([C@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 11, 22, 22, 4, 11, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 66, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476035 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476035 Building ZINC000804476036 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476036 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/909 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476036 none Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 11, 21, 21, 4, 11, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 63, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/910 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476036 none Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 28, 27, 10, 27, 27, 3, 10, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 81, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476036 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 Building ZINC000804476036 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476036 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 909) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476036 none Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 11, 21, 21, 4, 11, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 63, 11, 11, 11, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 910) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476036 none Cc1ccc([C@@H](O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 28, 27, 10, 27, 27, 3, 10, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 81, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476036 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476036 Building ZINC000804476037 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476037 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/911 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476037 none Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 28, 26, 13, 26, 26, 3, 13, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 78, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/912 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476037 none Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 30, 30, 25, 12, 25, 25, 3, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 75, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476037 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 Building ZINC000804476037 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804476037 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 911) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804476037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476037 none Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 28, 26, 13, 26, 26, 3, 13, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 78, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 912) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000804476037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804476037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000804476037 none Cc1ccc([C@@H](O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 30, 30, 25, 12, 25, 25, 3, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 75, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804476037 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804476037 Building ZINC000522253112 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522253112 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/913 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)o1) `ZINC000522253112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522253112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000522253112 none Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [47, 47, 47, 47, 28, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 28, 28, 17, 17, 4, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/914 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)o1) `ZINC000522253112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522253112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000522253112 none Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [47, 47, 47, 47, 28, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 28, 28, 17, 17, 4, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000522253112 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 Building ZINC000522253112 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522253112 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 913) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)o1) `ZINC000522253112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522253112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000522253112 none Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [47, 47, 47, 47, 28, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 28, 28, 17, 17, 4, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 914) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)o1) `ZINC000522253112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522253112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000522253112 none Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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: [47, 47, 47, 47, 28, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 28, 28, 17, 17, 4, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000522253112 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000522253112 Building ZINC000863846639 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000863846639 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/915 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(OCC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000863846639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000863846639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC000863846639 none CN(OCC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 29, 35, 35, 35, 35, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 13, 35, 35, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/916 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(OCC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000863846639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000863846639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC000863846639 none CN(OCC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 27, 36, 36, 36, 36, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 36, 36, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000863846639 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 Building ZINC000863846639 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000863846639 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 915) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(OCC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000863846639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000863846639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC000863846639 none CN(OCC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 29, 35, 35, 35, 35, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 13, 35, 35, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 916) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(OCC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000863846639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000863846639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 28 natoms 27 natoms 26 natoms 25 names: ZINC000863846639 none CN(OCC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 27, 36, 36, 36, 36, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 36, 36, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000863846639 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000863846639 Building ZINC000425600643 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425600643 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/917 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425600643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600643 none CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 7 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/918 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425600643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600643 none CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3] 6 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425600643 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 Building ZINC000425600643 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425600643 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 917) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425600643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600643 none CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 7 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 918) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425600643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600643 none CN(C)C[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3] 6 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425600643 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600643 Building ZINC000425600644 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425600644 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/919 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425600644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600644 none CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3] 11 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/920 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425600644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600644 none CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 16 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425600644 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 Building ZINC000425600644 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425600644 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 919) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425600644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600644 none CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3] 11 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 920) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000425600644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425600644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000425600644 none CN(C)C[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 16 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425600644 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425600644 Building ZINC000440448284 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440448284 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/921 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000440448284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440448284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000440448284 none CCOCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 8, 27, 27, 27, 27, 27, 18, 18, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/922 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000440448284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440448284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000440448284 none CCOCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 18, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 26, 26, 26, 26, 26, 18, 18, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000440448284 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 Building ZINC000440448284 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440448284 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 921) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000440448284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440448284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000440448284 none CCOCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 8, 27, 27, 27, 27, 27, 18, 18, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 922) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000440448284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440448284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000440448284 none CCOCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 18, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 26, 26, 26, 26, 26, 18, 18, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000440448284 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000440448284 Building ZINC000650910709 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650910709 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/923 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/923' -> `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)N1CCc2ccc(F)cc2[C@H](C)C1) `ZINC000650910709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650910709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910709 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/924 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/924' -> `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)N1CCc2ccc(F)cc2[C@H](C)C1) `ZINC000650910709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650910709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910709 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650910709 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 Building ZINC000650910709 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650910709 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 923) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@H](C)C1) `ZINC000650910709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650910709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910709 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 924) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@H](C)C1) `ZINC000650910709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650910709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910709 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650910709 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910709 Building ZINC000650910710 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650910710 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/925 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/925' -> `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)N1CCc2ccc(F)cc2[C@@H](C)C1) `ZINC000650910710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650910710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910710 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 50 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/926 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/926' -> `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)N1CCc2ccc(F)cc2[C@@H](C)C1) `ZINC000650910710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650910710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910710 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 17, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650910710 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 Building ZINC000650910710 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650910710 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 925) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@@H](C)C1) `ZINC000650910710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650910710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910710 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 50 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 926) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@@H](C)C1) `ZINC000650910710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650910710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000650910710 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 17, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650910710 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650910710 Building ZINC000650914614 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650914614 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/927 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650914614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914614 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/928 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650914614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914614 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650914614 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 Building ZINC000650914614 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650914614 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 927) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650914614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914614 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 928) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650914614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914614 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650914614 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914614 Building ZINC000650914615 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650914615 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/929 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650914615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914615 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/930 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650914615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914615 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650914615 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 Building ZINC000650914615 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650914615 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 929) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650914615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914615 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 14, 14, 14, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 930) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl) `ZINC000650914615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650914615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000650914615 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CC3(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 15, 15, 15, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650914615 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650914615 Building ZINC000650920162 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650920162 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/931 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650920162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920162 none O=C(N1CC[C@@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 1, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 20 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/932 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650920162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920162 none O=C(N1CC[C@@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 2, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 22 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650920162 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 Building ZINC000650920162 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650920162 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 931) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650920162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920162 none O=C(N1CC[C@@]2(CC2(F)F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 1, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5] 20 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 932) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000650920162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650920162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000650920162 none O=C(N1CC[C@@]2(CC2(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 5, 5, 1, 2, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 22 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000650920162 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000650920162 Building ZINC000174458460 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000174458460 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/933 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/934 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/935 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/935' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/936 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/936' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174458460 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 Building ZINC000174458460 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000174458460 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 933) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 934) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 935) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 936) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174458460 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 Building ZINC000174458460 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000174458460 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 933) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 934) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 935) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 936) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174458460 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 Building ZINC000174458460 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000174458460 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 933) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 934) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 1, 9, 9, 1, 1, 1, 3, 12, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9] 34 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `2' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 2 (index: 935) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `3' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 3 (index: 936) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1) `ZINC000174458460.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000174458460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000174458460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C)c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 1, 10, 10, 1, 1, 1, 3, 15, 26, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10] 39 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000174458460 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/0.* 3: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/3.* 2: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460/2.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000174458460 Building ZINC000425986196 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425986196 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/937 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21) `ZINC000425986196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425986196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000425986196 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 47, 19, 50, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 4, 3, 3, 3, 3, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/938 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21) `ZINC000425986196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425986196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000425986196 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 47, 19, 50, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 4, 3, 3, 3, 3, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425986196 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 Building ZINC000425986196 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000425986196 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 937) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21) `ZINC000425986196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000425986196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000425986196 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 47, 19, 50, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 4, 3, 3, 3, 3, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 938) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21) `ZINC000425986196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000425986196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000425986196 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc2[nH]ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 47, 19, 50, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 4, 3, 3, 3, 3, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000425986196 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000425986196 Building ZINC001131737031 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001131737031 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/939 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OC) `ZINC001131737031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001131737031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001131737031 none COCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 10, 10, 10, 23, 44, 44, 44, 41, 41, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 10, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/940 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OC) `ZINC001131737031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001131737031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001131737031 none COCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 10, 10, 10, 23, 44, 44, 44, 41, 41, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 10, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001131737031 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 Building ZINC001131737031 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001131737031 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 939) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OC) `ZINC001131737031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001131737031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001131737031 none COCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 10, 10, 10, 23, 44, 44, 44, 41, 41, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 10, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 940) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OC) `ZINC001131737031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001131737031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001131737031 none COCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 10, 10, 10, 23, 44, 44, 44, 41, 41, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 10, 23, 23, 23] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC001131737031 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC001131737031 Building ZINC000426097715 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426097715 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/941 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426097715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426097715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000426097715 none CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 9, 16, 16, 25, 4, 9, 28, 32, 32, 30, 32, 32, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 21, 21, 21, 21, 25, 25, 75, 28, 28, 32, 32, 32, 32, 32, 2, 2, 2, 2] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 304 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/942 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426097715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426097715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000426097715 none CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 10, 16, 16, 26, 5, 10, 26, 28, 28, 27, 28, 28, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 20, 20, 20, 26, 26, 78, 26, 26, 28, 28, 28, 28, 28, 3, 3, 3, 3] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 287 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426097715 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 Building ZINC000426097715 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426097715 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 941) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426097715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426097715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000426097715 none CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 9, 16, 16, 25, 4, 9, 28, 32, 32, 30, 32, 32, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 21, 21, 21, 21, 25, 25, 75, 28, 28, 32, 32, 32, 32, 32, 2, 2, 2, 2] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 304 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 942) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426097715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426097715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000426097715 none CC[C@@H](CO)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 10, 16, 16, 26, 5, 10, 26, 28, 28, 27, 28, 28, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 20, 20, 20, 26, 26, 78, 26, 26, 28, 28, 28, 28, 28, 3, 3, 3, 3] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 287 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426097715 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426097715 Building ZINC000618607310 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618607310 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/943 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F) `ZINC000618607310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618607310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000618607310 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 4, 5, 5, 42, 42, 42, 42, 42, 42, 42, 26, 26, 6, 5, 5, 5, 5, 42, 42] 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]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/944 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F) `ZINC000618607310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618607310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000618607310 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 26, 26, 6, 5, 5, 5, 5, 42, 42] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618607310 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 Building ZINC000618607310 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618607310 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 943) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F) `ZINC000618607310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618607310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000618607310 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 4, 5, 5, 42, 42, 42, 42, 42, 42, 42, 26, 26, 6, 5, 5, 5, 5, 42, 42] 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]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 944) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F) `ZINC000618607310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618607310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000618607310 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 26, 26, 6, 5, 5, 5, 5, 42, 42] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618607310 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618607310 Building ZINC000426280570 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426280570 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/945 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426280570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280570 none CC1(C)CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 30, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 22, 22, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/946 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426280570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280570 none CC1(C)CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 29, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426280570 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 Building ZINC000426280570 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426280570 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 945) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426280570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280570 none CC1(C)CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 30, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 22, 22, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 946) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426280570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280570 none CC1(C)CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 29, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426280570 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280570 Building ZINC000426280571 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426280571 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/947 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426280571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280571 none CC1(C)CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 29, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/948 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426280571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280571 none CC1(C)CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 29, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 21, 21, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426280571 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 Building ZINC000426280571 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426280571 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 947) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426280571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280571 none CC1(C)CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 29, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 948) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1) `ZINC000426280571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426280571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000426280571 none CC1(C)CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 29, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 21, 21, 4, 3, 3, 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, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426280571 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426280571 Building ZINC000426295758 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426295758 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/949 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426295758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426295758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000426295758 none O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 41, 47, 47, 47, 41, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 4, 6, 6, 11, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/950 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426295758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426295758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000426295758 none O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 41, 47, 47, 47, 41, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426295758 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 Building ZINC000426295758 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426295758 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 949) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426295758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426295758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000426295758 none O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 41, 47, 47, 47, 41, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 4, 6, 6, 11, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 950) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000426295758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426295758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000426295758 none O=C(Nc1cc2c(cc1F)NC(=O)CC2)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 41, 47, 47, 47, 41, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426295758 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426295758 Building ZINC000426321717 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426321717 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/951 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426321717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321717 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 17, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 11, 11, 11, 4, 4, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/952 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426321717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321717 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426321717 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 Building ZINC000426321717 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426321717 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 951) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426321717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321717 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 17, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 11, 11, 11, 4, 4, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 952) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426321717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321717 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426321717 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321717 Building ZINC000426321726 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426321726 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/953 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426321726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321726 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/954 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426321726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321726 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 17, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 11, 11, 11, 4, 4, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426321726 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 Building ZINC000426321726 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426321726 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 953) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426321726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321726 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 954) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl) `ZINC000426321726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426321726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000426321726 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)O2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 17, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 11, 11, 11, 4, 4, 2, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426321726 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426321726 Building ZINC000426371796 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426371796 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/955 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000426371796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426371796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000426371796 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 6, 21, 21, 21, 22, 22, 21, 22, 22, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/956 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000426371796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426371796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000426371796 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 7, 21, 21, 21, 29, 29, 21, 29, 29, 7, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 21, 29, 29, 21, 29, 29, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426371796 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 Building ZINC000426371796 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426371796 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 955) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000426371796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426371796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000426371796 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 6, 21, 21, 21, 22, 22, 21, 22, 22, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 21, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 956) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000426371796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426371796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000426371796 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 7, 21, 21, 21, 29, 29, 21, 29, 29, 7, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 21, 29, 29, 21, 29, 29, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426371796 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426371796 Building ZINC000426366928 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426366928 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/957 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000426366928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426366928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000426366928 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 33, 33, 33, 49, 49, 33, 49, 49, 9, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 33, 49, 49, 34, 49, 49, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/958 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000426366928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426366928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000426366928 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 34, 34, 34, 48, 48, 34, 48, 48, 9, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 34, 48, 48, 38, 48, 48, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426366928 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 Building ZINC000426366928 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426366928 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 957) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000426366928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426366928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000426366928 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 33, 33, 33, 49, 49, 33, 49, 49, 9, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 33, 49, 49, 34, 49, 49, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 958) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000426366928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426366928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000426366928 none O=C(NC1(C(=O)Nc2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 34, 34, 34, 48, 48, 34, 48, 48, 9, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 34, 48, 48, 38, 48, 48, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426366928 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426366928 Building ZINC000426405408 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426405408 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/959 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1) `ZINC000426405408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426405408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000426405408 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 7, 7, 7, 11, 35, 35, 35, 44, 44, 35, 44, 44, 11, 11, 3, 3, 3, 3, 3, 3, 7, 35, 44, 44, 38, 44, 44, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/960 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1) `ZINC000426405408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426405408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000426405408 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 10, 37, 37, 37, 46, 46, 37, 46, 46, 10, 10, 3, 3, 3, 3, 3, 3, 6, 37, 46, 46, 43, 46, 46, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426405408 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 Building ZINC000426405408 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426405408 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 959) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1) `ZINC000426405408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426405408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000426405408 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 7, 7, 7, 11, 35, 35, 35, 44, 44, 35, 44, 44, 11, 11, 3, 3, 3, 3, 3, 3, 7, 35, 44, 44, 38, 44, 44, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 960) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1) `ZINC000426405408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426405408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000426405408 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC1(C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 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, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 10, 37, 37, 37, 46, 46, 37, 46, 46, 10, 10, 3, 3, 3, 3, 3, 3, 6, 37, 46, 46, 43, 46, 46, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426405408 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426405408 Building ZINC000523693445 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523693445 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/961 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000523693445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523693445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000523693445 none CC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 44, 44, 37, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 37, 37, 23, 23, 4, 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: 191 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/962 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000523693445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523693445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000523693445 none CC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 45, 45, 39, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 39, 39, 25, 25, 4, 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: 186 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000523693445 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 Building ZINC000523693445 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523693445 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 961) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000523693445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523693445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000523693445 none CC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 44, 44, 37, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 37, 37, 23, 23, 4, 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: 191 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 962) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000523693445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523693445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000523693445 none CC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 45, 45, 39, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 39, 39, 25, 25, 4, 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: 186 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000523693445 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000523693445 Building ZINC000618691543 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618691543 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/963 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618691543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691543 none O=C(N1CCC[C@@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 12, 12, 12, 12, 12, 25, 32, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 25, 25, 32, 32, 12, 12, 6, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/964 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618691543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691543 none O=C(N1CCC[C@@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 12, 12, 12, 12, 12, 12, 24, 29, 12, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 12, 12, 6, 11, 11, 6, 11, 11, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618691543 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 Building ZINC000618691543 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618691543 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 963) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618691543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691543 none O=C(N1CCC[C@@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 12, 12, 12, 12, 12, 25, 32, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 25, 25, 32, 32, 12, 12, 6, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 964) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618691543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691543 none O=C(N1CCC[C@@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 12, 12, 12, 12, 12, 12, 24, 29, 12, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 12, 12, 6, 11, 11, 6, 11, 11, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618691543 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691543 Building ZINC000618691544 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618691544 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/965 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618691544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691544 none O=C(N1CCC[C@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 12, 12, 12, 12, 12, 12, 25, 30, 12, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12, 12, 12, 25, 25, 30, 30, 12, 12, 6, 11, 11, 6, 11, 11, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/966 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618691544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691544 none O=C(N1CCC[C@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 12, 12, 12, 12, 12, 25, 32, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 25, 25, 32, 32, 12, 12, 6, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618691544 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 Building ZINC000618691544 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618691544 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 965) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618691544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691544 none O=C(N1CCC[C@H](CCF)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 12, 12, 12, 12, 12, 12, 25, 30, 12, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 12, 12, 12, 12, 12, 12, 25, 25, 30, 30, 12, 12, 6, 11, 11, 6, 11, 11, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 966) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000618691544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618691544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000618691544 none O=C(N1CCC[C@H](CCF)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 12, 12, 12, 12, 12, 25, 32, 12, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 12, 12, 12, 12, 12, 12, 25, 25, 32, 32, 12, 12, 6, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618691544 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618691544 Building ZINC000078077316 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000078077316 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/967 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1) `ZINC000078077316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000078077316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000078077316 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 14, 14, 14, 38, 38, 8, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 38, 38, 38, 38, 38, 8, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/968 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1) `ZINC000078077316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000078077316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000078077316 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 14, 14, 14, 40, 40, 8, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 40, 40, 40, 40, 40, 8, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000078077316 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 Building ZINC000078077316 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000078077316 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 967) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1) `ZINC000078077316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000078077316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000078077316 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 14, 14, 14, 38, 38, 8, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 38, 38, 38, 38, 38, 8, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 968) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1) `ZINC000078077316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000078077316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000078077316 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC(=O)C3CC3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 14, 14, 14, 40, 40, 8, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 40, 40, 40, 40, 40, 8, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000078077316 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000078077316 Building ZINC000158539974 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158539974 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/969 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1) `ZINC000158539974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158539974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158539974 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 11, 11, 21, 26, 11, 16, 16, 11, 16, 16, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 26, 26, 78, 16, 16, 12, 16, 16] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/970 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1) `ZINC000158539974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158539974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158539974 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 24, 26, 14, 17, 17, 14, 17, 17, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 26, 26, 78, 17, 17, 14, 17, 17] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158539974 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 Building ZINC000158539974 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158539974 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 969) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1) `ZINC000158539974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158539974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158539974 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 11, 11, 21, 26, 11, 16, 16, 11, 16, 16, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 26, 26, 78, 16, 16, 12, 16, 16] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 970) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1) `ZINC000158539974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158539974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158539974 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 24, 26, 14, 17, 17, 14, 17, 17, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 26, 26, 78, 17, 17, 14, 17, 17] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 212 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158539974 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158539974 Building ZINC000158540126 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158540126 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/971 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1) `ZINC000158540126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158540126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158540126 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 23, 25, 13, 16, 16, 16, 16, 16, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 25, 25, 75, 16, 16, 13, 16, 16] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/972 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1) `ZINC000158540126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158540126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158540126 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 11, 11, 21, 26, 11, 16, 16, 11, 16, 16, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 26, 26, 78, 16, 16, 11, 16, 16] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158540126 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 Building ZINC000158540126 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000158540126 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 971) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1) `ZINC000158540126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000158540126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158540126 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 23, 25, 13, 16, 16, 16, 16, 16, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 25, 25, 75, 16, 16, 13, 16, 16] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 972) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1) `ZINC000158540126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000158540126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000158540126 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)[C@H](CCO)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 11, 11, 21, 26, 11, 16, 16, 11, 16, 16, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 26, 26, 78, 16, 16, 11, 16, 16] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000158540126 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000158540126 Building ZINC000426908673 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426908673 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/973 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426908673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908673 none C[C@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 10, 21, 21, 29, 29, 25, 29, 29, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 7, 7, 7, 10, 10, 29, 29, 29, 29, 29, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/974 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426908673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908673 none C[C@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 22, 22, 29, 29, 25, 29, 29, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 12, 12, 29, 29, 29, 29, 29, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426908673 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 Building ZINC000426908673 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426908673 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 973) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426908673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908673 none C[C@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 10, 21, 21, 29, 29, 25, 29, 29, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 7, 7, 7, 10, 10, 29, 29, 29, 29, 29, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 974) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426908673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908673 none C[C@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 22, 22, 29, 29, 25, 29, 29, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 12, 12, 29, 29, 29, 29, 29, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426908673 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908673 Building ZINC000426908674 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426908674 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/975 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426908674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908674 none C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 23, 23, 32, 32, 25, 32, 32, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 6, 6, 6, 12, 12, 32, 32, 32, 32, 32, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/976 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426908674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908674 none C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 10, 22, 22, 29, 29, 26, 29, 29, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 7, 10, 10, 29, 29, 29, 29, 29, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426908674 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 Building ZINC000426908674 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000426908674 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 975) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000426908674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908674 none C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 23, 23, 32, 32, 25, 32, 32, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 6, 6, 6, 12, 12, 32, 32, 32, 32, 32, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 976) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000426908674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000426908674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000426908674 none C[C@@H](CC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 10, 22, 22, 29, 29, 26, 29, 29, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 7, 7, 10, 10, 29, 29, 29, 29, 29, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000426908674 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000426908674 Building ZINC000152318252 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152318252 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/977 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152318252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152318252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000152318252 none CN(CCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 24, 24, 27, 27, 27, 27, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/978 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152318252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152318252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000152318252 none CN(CCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 22, 22, 26, 26, 26, 26, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152318252 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 Building ZINC000152318252 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152318252 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 977) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152318252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152318252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000152318252 none CN(CCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 24, 24, 27, 27, 27, 27, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 978) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000152318252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152318252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000152318252 none CN(CCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 6, 6, 22, 22, 26, 26, 26, 26, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000152318252 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000152318252 Building ZINC000427035551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427035551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/979 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1) `ZINC000427035551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427035551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000427035551 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 16, 26, 26, 26, 16, 26, 26, 26, 26, 26, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/980 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1) `ZINC000427035551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427035551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000427035551 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 24, 24, 24, 16, 24, 24, 24, 24, 24, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000427035551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 Building ZINC000427035551 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000427035551 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 979) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1) `ZINC000427035551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000427035551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000427035551 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 16, 26, 26, 26, 16, 26, 26, 26, 26, 26, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 980) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1) `ZINC000427035551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000427035551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000427035551 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)C(=O)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 7, 7, 1, 1, 1, 1, 4, 4, 4, 16, 24, 24, 24, 16, 24, 24, 24, 24, 24, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000427035551 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000427035551 Building ZINC000618838766 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618838766 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/981 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1) `ZINC000618838766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618838766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000618838766 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 13, 23, 23, 23, 13, 23, 23, 23, 23, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 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, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/982 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1) `ZINC000618838766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618838766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000618838766 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 15, 24, 24, 24, 15, 24, 24, 24, 24, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618838766 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 Building ZINC000618838766 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618838766 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 981) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1) `ZINC000618838766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618838766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000618838766 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 13, 23, 23, 23, 13, 23, 23, 23, 23, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 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, 42, 43, 44]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 982) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1) `ZINC000618838766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618838766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000618838766 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CCOC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 15, 24, 24, 24, 15, 24, 24, 24, 24, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618838766 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618838766 Building ZINC000804804335 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804804335 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/983 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804804335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804335 none C[C@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 26, 26, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 11, 11, 8, 8, 26, 26, 26, 78, 11, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 11, 11] 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, 42, 43]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/984 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804804335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804335 none C[C@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 24, 24, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 10, 10, 2, 2, 24, 24, 24, 72, 10, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 10, 10] 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, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804804335 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 Building ZINC000804804335 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804804335 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 983) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804804335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804335 none C[C@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 26, 26, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 11, 11, 8, 8, 26, 26, 26, 78, 11, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 11, 11] 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, 42, 43]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 984) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804804335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804335 none C[C@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 24, 24, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 10, 10, 2, 2, 24, 24, 24, 72, 10, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 10, 10] 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, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804804335 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804335 Building ZINC000804804337 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804804337 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/985 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804804337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804337 none C[C@@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 24, 24, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 10, 10, 8, 8, 24, 24, 24, 72, 10, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 10, 10] 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, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/986 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804804337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804337 none C[C@@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 24, 24, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 11, 11, 4, 8, 24, 24, 24, 72, 11, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 11, 11] 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, 42, 43]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804804337 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 Building ZINC000804804337 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000804804337 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 985) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000804804337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804337 none C[C@@H](O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 24, 24, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 10, 10, 8, 8, 24, 24, 24, 72, 10, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 10, 10] 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, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 986) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F) `ZINC000804804337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000804804337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000804804337 none C[C@@H](O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 24, 24, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 11, 11, 4, 8, 24, 24, 24, 72, 11, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 11, 11] 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, 42, 43]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000804804337 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000804804337 Building ZINC000618891251 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618891251 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/987 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1) `ZINC000618891251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618891251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000618891251 none Cc1ccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 8, 8, 8, 1, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 8, 27, 27, 27, 27, 27, 27, 27, 26, 26, 8, 8, 8, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 8, 8, 27, 27] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/988 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1) `ZINC000618891251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618891251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000618891251 none Cc1ccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 9, 9, 9, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 4, 9, 27, 27, 27, 27, 27, 27, 27, 26, 26, 9, 9, 9, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 9, 9, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618891251 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 Building ZINC000618891251 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618891251 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 987) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1) `ZINC000618891251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618891251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000618891251 none Cc1ccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 8, 8, 8, 1, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 8, 27, 27, 27, 27, 27, 27, 27, 26, 26, 8, 8, 8, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 8, 8, 27, 27] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 988) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1) `ZINC000618891251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618891251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000618891251 none Cc1ccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 9, 9, 9, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 4, 9, 27, 27, 27, 27, 27, 27, 27, 26, 26, 9, 9, 9, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 9, 9, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618891251 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618891251 Building ZINC000618898345 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618898345 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/989 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O) `ZINC000618898345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618898345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000618898345 none CN1CCc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/990 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O) `ZINC000618898345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618898345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000618898345 none CN1CCc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618898345 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 Building ZINC000618898345 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000618898345 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 989) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O) `ZINC000618898345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000618898345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000618898345 none CN1CCc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 24, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 24, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 990) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O) `ZINC000618898345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000618898345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000618898345 none CN1CCc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000618898345 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000618898345 Building ZINC000190698773 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190698773 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/991 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/991' -> `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(F)(F)F)C(C)(C)C1) `ZINC000190698773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190698773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190698773 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.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, 7, 5, 15, 15, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 15, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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, 45]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/992 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/992' -> `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(F)(F)F)C(C)(C)C1) `ZINC000190698773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190698773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190698773 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.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, 7, 5, 15, 15, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 16, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000190698773 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 Building ZINC000190698773 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190698773 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 991) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C(C)(C)C1) `ZINC000190698773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190698773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190698773 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.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, 7, 5, 15, 15, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 15, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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, 45]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 992) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C(C)(C)C1) `ZINC000190698773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190698773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190698773 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.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, 7, 5, 15, 15, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 16, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000190698773 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000190698773 Building ZINC000343313062 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343313062 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/993 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343313062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343313062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343313062 none COc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 17, 17, 7, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 17, 17, 17, 33, 33, 33, 17, 17, 7, 7, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/994 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343313062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343313062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343313062 none COc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 17, 17, 7, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 17, 17, 17, 26, 26, 26, 17, 17, 7, 7, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343313062 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 Building ZINC000343313062 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343313062 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 993) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343313062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343313062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343313062 none COc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 17, 17, 7, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 17, 17, 17, 33, 33, 33, 17, 17, 7, 7, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 994) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343313062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343313062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343313062 none COc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 17, 17, 7, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 17, 17, 17, 26, 26, 26, 17, 17, 7, 7, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 17, 17, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343313062 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343313062 Building ZINC000343319917 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343319917 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/995 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000343319917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343319917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343319917 none COc1ccccc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/996 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000343319917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343319917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343319917 none COc1ccccc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343319917 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 Building ZINC000343319917 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343319917 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 995) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000343319917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343319917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343319917 none COc1ccccc1C(C)(C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 996) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000343319917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343319917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000343319917 none COc1ccccc1C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000343319917 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000343319917 Building ZINC000568916736 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568916736 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/997 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000568916736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568916736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000568916736 none O=C(NCCc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 21, 26, 26, 21, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 21, 21, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/998 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000568916736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568916736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000568916736 none O=C(NCCc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 21, 26, 26, 21, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 21, 21, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000568916736 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 Building ZINC000568916736 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568916736 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 997) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000568916736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568916736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000568916736 none O=C(NCCc1ccc(F)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 21, 26, 26, 21, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 21, 21, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 998) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000568916736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568916736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000568916736 none O=C(NCCc1ccc(F)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 21, 26, 26, 21, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 21, 21, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000568916736 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000568916736 Building ZINC000839734207 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734207 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/999 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)O1) `ZINC000839734207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000839734207 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23] 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: 56 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/74215/xan-8058115.14/working/3D/1000 `/scratch/xiaobo/74215/xan-8058115.14/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)O1) `ZINC000839734207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000839734207 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 3, 17, 1, 1, 1, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 24, 24, 24, 24, 24, 24] 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: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000839734207 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 Building ZINC000839734207 mkdir: created directory `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734207 mkdir: created directory `0' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/0 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 0 (index: 999) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)O1) `ZINC000839734207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000839734207 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 23, 23, 23, 23, 23, 23] 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: 56 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 mkdir: created directory `1' /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/1 /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Protomer 1 (index: 1000) grep: /scratch/xiaobo/74215/xan-8058115.14/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)O1) `ZINC000839734207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000839734207 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](C)[C@H](C)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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 3, 17, 1, 1, 1, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 24, 24, 24, 24, 24, 24] 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: 59 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Finished preparing ZINC000839734207 Recording results /scratch/xiaobo/74215/xan-8058115.14/working /scratch/xiaobo/74215/xan-8058115.14 Appending to /scratch/xiaobo/74215/xan-8058115.14/finished/xan.* 1: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/1.* 0: /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207/0.* Removing working files in /scratch/xiaobo/74215/xan-8058115.14/working/building/ZINC000839734207 /scratch/xiaobo/74215/xan-8058115.14 Compressing combined databse files /scratch/xiaobo/74215/xan-8058115.14/finished/xan.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/74215/xan-8058115.14/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/74215/xan-8058115.14/working/3D/1001' removed directory: `/scratch/xiaobo/74215/xan-8058115.14/working/3D' rmdir: removing directory, `/scratch/xiaobo/74215/xan-8058115.14/working/building' rmdir: removing directory, `/scratch/xiaobo/74215/xan-8058115.14/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/74215/xan-8058115.14' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xan' `/scratch/xiaobo/74215/xan-8058115.14/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xan/finished' `/scratch/xiaobo/74215/xan-8058115.14/finished/xan.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xan/finished/xan.db2.gz' removed `/scratch/xiaobo/74215/xan-8058115.14/finished/xan.db2.gz' removed directory: `/scratch/xiaobo/74215/xan-8058115.14/finished' removed directory: `/scratch/xiaobo/74215/xan-8058115.14'